encode_decode_experiment.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "id": "initial_id",
   "metadata": {
    "collapsed": true,
    "ExecuteTime": {
     "end_time": "2024-05-21T08:54:09.409531Z",
     "start_time": "2024-05-21T08:54:08.482270Z"
    }
   },
   "source": [
    "import base64\n",
    "import glob\n",
    "from NOREC4DNA.norec4dna import get_error_correction_decode, RU10Decoder, RU10Encoder, get_error_correction_encode\n",
    "from NOREC4DNA.norec4dna.distributions.RaptorDistribution import RaptorDistribution\n",
    "from cluster_exp import raptor_dist, bmp_low_entropy_evo_dist, bmp_low_entropy_diff_dist, \\\n",
    "    evo_compress_encrypt_high_entropy_dist, diff_compress_encrypt_high_entropy_dist\n",
    "from NOREC4DNA.norec4dna.helper.RU10Helper import intermediate_symbols\n"
   ],
   "outputs": [],
   "execution_count": 1
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-21T14:39:00.436601Z",
     "start_time": "2024-05-21T13:06:20.928793Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from NOREC4DNA.norec4dna.rules.FastDNARules import FastDNARules\n",
    "def encode_to_fasta(filename, number_of_chunks, error_correction, use_seed_xor, use_payload_xor, seed_spacing, use_headerchunk, in_dist):\n",
    "    dist = RaptorDistribution(number_of_chunks)\n",
    "    dist.f = in_dist\n",
    "    dist.d = [x for x in range(0, 41)]\n",
    "    encoder = RU10Encoder(filename, number_of_chunks, dist, insert_header=use_headerchunk, pseudo_decoder=None,\n",
    "                 rules=FastDNARules(), error_correction=error_correction, packet_len_format=\"I\", crc_len_format=\"I\",\n",
    "                 number_of_chunks_len_format=\"I\", id_len_format=\"I\", save_number_of_chunks_in_packet=False,\n",
    "                 mode_1_bmp=False, prepend=\"\", append=\"\", drop_upper_bound=1.0, keep_all_packets=False,\n",
    "                 checksum_len_str=None, xor_by_seed=use_payload_xor, mask_id=use_seed_xor, id_spacing=seed_spacing)\n",
    "    encoder.set_overhead_limit(1.0)\n",
    "    encoder.encode_to_packets()\n",
    "    encoder.save_packets_fasta(\"out_file\", seed_is_filename=True)\n",
    "    return encoder\n",
    "\n",
    "encoder = encode_to_fasta(\"sleeping_beauty\", 289, get_error_correction_encode(\"reedsolomon\",2), False, True, 2, False, raptor_dist)\n",
    "\n",
    "def decode_from_fasta(filename, number_of_chunks, dist, error_correction, use_seed_xor, use_payload_xor, seed_spacing,\n",
    "                      use_headerchunk):\n",
    "    decoder = RU10Decoder(file=filename, error_correction=error_correction, use_headerchunk=use_headerchunk,\n",
    "                          static_number_of_chunks=number_of_chunks, checksum_len_str=None,\n",
    "                          xor_by_seed=use_payload_xor, mask_id=use_seed_xor, id_spacing=seed_spacing)\n",
    "\n",
    "    decoder.distribution = RaptorDistribution(number_of_chunks)\n",
    "    # update distribution.f:\n",
    "    decoder.distribution.f = dist\n",
    "    decoder.distribution.d = [x for x in range(0, 41)]\n",
    "    decoder.number_of_chunks = number_of_chunks\n",
    "    _, decoder.s, decoder.h = intermediate_symbols(number_of_chunks, decoder.distribution)\n",
    "    decoder.createAuxBlocks()\n",
    "    decoder.progress_bar = decoder.create_progress_bar(number_of_chunks + 0.02 * number_of_chunks)\n",
    "    res = decoder.decodeFile(id_len_format=\"I\")\n",
    "    print(f\"Success: {res}\")\n",
    "    res_data = decoder.saveDecodedFile(last_chunk_len_format=\"\", null_is_terminator=False, print_to_output=False,\n",
    "                            partial_decoding=True)\n",
    "    return res, res_data\n",
    "\n",
    "decode_from_fasta(\"out_file.fasta\", 289, raptor_dist, get_error_correction_decode(\"reedsolomon\", 2), False, True, 2, False)\n",
    "\n",
    "def get_dist(filename):\n",
    "    if \"raptor\" in filename:\n",
    "        return raptor_dist, \"raptor\"\n",
    "    elif \"low_entropy_evo\" in filename:\n",
    "        return bmp_low_entropy_evo_dist, \"low_entropy_evo\"\n",
    "    elif \"low_entropy_diff\" in filename:\n",
    "        return bmp_low_entropy_diff_dist, \"low_entropy_diff\"\n",
    "    elif \"evo_compress_encrypt\" in filename:\n",
    "        return evo_compress_encrypt_high_entropy_dist, \"evo_compress_encrypt\"\n",
    "    elif \"diff_compress_encrypt\" in filename:\n",
    "        return diff_compress_encrypt_high_entropy_dist, \"diff_compress_encrypt\"\n",
    "    else:\n",
    "        raise ValueError(\"Unknown dist\")\n",
    "\n",
    "\n",
    "def get_seed_spacing(filename):\n",
    "    if not \"seedspacing\" in filename:\n",
    "        return 0\n",
    "    else:\n",
    "        return int(filename.replace(\"_payloadxor\", \"\").split(\"seedspacing\")[1].split(\".\")[0])\n",
    "\n",
    "\n",
    "def get_payload_xor(filename):\n",
    "    return \"_payloadxor\" in filename"
   ],
   "id": "db9d2b5aa9b24b0f",
   "outputs": [
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
      "\u001B[0;31mKeyboardInterrupt\u001B[0m                         Traceback (most recent call last)",
      "Cell \u001B[0;32mIn[125], line 38\u001B[0m\n\u001B[1;32m     34\u001B[0m     res_data \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39msaveDecodedFile(last_chunk_len_format\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m\"\u001B[39m, null_is_terminator\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mFalse\u001B[39;00m, print_to_output\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mFalse\u001B[39;00m,\n\u001B[1;32m     35\u001B[0m                             partial_decoding\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mTrue\u001B[39;00m)\n\u001B[1;32m     36\u001B[0m     \u001B[38;5;28;01mreturn\u001B[39;00m res, res_data\n\u001B[0;32m---> 38\u001B[0m \u001B[43mdecode_from_fasta\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mout_file.fasta\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m289\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mraptor_dist\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mget_error_correction_decode\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mreedsolomon\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m2\u001B[39;49m\u001B[43m)\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m2\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m)\u001B[49m\n\u001B[1;32m     40\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mget_dist\u001B[39m(filename):\n\u001B[1;32m     41\u001B[0m     \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mraptor\u001B[39m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;129;01min\u001B[39;00m filename:\n",
      "Cell \u001B[0;32mIn[125], line 30\u001B[0m, in \u001B[0;36mdecode_from_fasta\u001B[0;34m(filename, number_of_chunks, dist, error_correction, use_seed_xor, use_payload_xor, seed_spacing, use_headerchunk)\u001B[0m\n\u001B[1;32m     28\u001B[0m decoder\u001B[38;5;241m.\u001B[39mnumber_of_chunks \u001B[38;5;241m=\u001B[39m number_of_chunks\n\u001B[1;32m     29\u001B[0m _, decoder\u001B[38;5;241m.\u001B[39ms, decoder\u001B[38;5;241m.\u001B[39mh \u001B[38;5;241m=\u001B[39m intermediate_symbols(number_of_chunks, decoder\u001B[38;5;241m.\u001B[39mdistribution)\n\u001B[0;32m---> 30\u001B[0m \u001B[43mdecoder\u001B[49m\u001B[38;5;241m.\u001B[39mcreateAuxBlocks()\n\u001B[1;32m     31\u001B[0m decoder\u001B[38;5;241m.\u001B[39mprogress_bar \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39mcreate_progress_bar(number_of_chunks \u001B[38;5;241m+\u001B[39m \u001B[38;5;241m0.02\u001B[39m \u001B[38;5;241m*\u001B[39m number_of_chunks)\n\u001B[1;32m     32\u001B[0m res \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39mdecodeFile(id_len_format\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mI\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n",
      "Cell \u001B[0;32mIn[125], line 30\u001B[0m, in \u001B[0;36mdecode_from_fasta\u001B[0;34m(filename, number_of_chunks, dist, error_correction, use_seed_xor, use_payload_xor, seed_spacing, use_headerchunk)\u001B[0m\n\u001B[1;32m     28\u001B[0m decoder\u001B[38;5;241m.\u001B[39mnumber_of_chunks \u001B[38;5;241m=\u001B[39m number_of_chunks\n\u001B[1;32m     29\u001B[0m _, decoder\u001B[38;5;241m.\u001B[39ms, decoder\u001B[38;5;241m.\u001B[39mh \u001B[38;5;241m=\u001B[39m intermediate_symbols(number_of_chunks, decoder\u001B[38;5;241m.\u001B[39mdistribution)\n\u001B[0;32m---> 30\u001B[0m \u001B[43mdecoder\u001B[49m\u001B[38;5;241m.\u001B[39mcreateAuxBlocks()\n\u001B[1;32m     31\u001B[0m decoder\u001B[38;5;241m.\u001B[39mprogress_bar \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39mcreate_progress_bar(number_of_chunks \u001B[38;5;241m+\u001B[39m \u001B[38;5;241m0.02\u001B[39m \u001B[38;5;241m*\u001B[39m number_of_chunks)\n\u001B[1;32m     32\u001B[0m res \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39mdecodeFile(id_len_format\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mI\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n",
      "File \u001B[0;32m~/.local/share/JetBrains/Toolbox/apps/pycharm-professional/plugins/python/helpers/pydev/_pydevd_bundle/pydevd_frame.py:755\u001B[0m, in \u001B[0;36mPyDBFrame.trace_dispatch\u001B[0;34m(self, frame, event, arg)\u001B[0m\n\u001B[1;32m    753\u001B[0m \u001B[38;5;66;03m# if thread has a suspend flag, we suspend with a busy wait\u001B[39;00m\n\u001B[1;32m    754\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m info\u001B[38;5;241m.\u001B[39mpydev_state \u001B[38;5;241m==\u001B[39m STATE_SUSPEND:\n\u001B[0;32m--> 755\u001B[0m     \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdo_wait_suspend\u001B[49m\u001B[43m(\u001B[49m\u001B[43mthread\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mframe\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mevent\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43marg\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    756\u001B[0m     \u001B[38;5;66;03m# No need to reset frame.f_trace to keep the same trace function.\u001B[39;00m\n\u001B[1;32m    757\u001B[0m     \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mtrace_dispatch\n",
      "File \u001B[0;32m~/.local/share/JetBrains/Toolbox/apps/pycharm-professional/plugins/python/helpers/pydev/_pydevd_bundle/pydevd_frame.py:412\u001B[0m, in \u001B[0;36mPyDBFrame.do_wait_suspend\u001B[0;34m(self, *args, **kwargs)\u001B[0m\n\u001B[1;32m    411\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mdo_wait_suspend\u001B[39m(\u001B[38;5;28mself\u001B[39m, \u001B[38;5;241m*\u001B[39margs, \u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mkwargs):\n\u001B[0;32m--> 412\u001B[0m     \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_args\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m0\u001B[39;49m\u001B[43m]\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdo_wait_suspend\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43margs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n",
      "File \u001B[0;32m~/.local/share/JetBrains/Toolbox/apps/pycharm-professional/plugins/python/helpers/pydev/pydevd.py:1184\u001B[0m, in \u001B[0;36mPyDB.do_wait_suspend\u001B[0;34m(self, thread, frame, event, arg, send_suspend_message, is_unhandled_exception)\u001B[0m\n\u001B[1;32m   1181\u001B[0m         from_this_thread\u001B[38;5;241m.\u001B[39mappend(frame_id)\n\u001B[1;32m   1183\u001B[0m \u001B[38;5;28;01mwith\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_threads_suspended_single_notification\u001B[38;5;241m.\u001B[39mnotify_thread_suspended(thread_id, stop_reason):\n\u001B[0;32m-> 1184\u001B[0m     \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m_do_wait_suspend\u001B[49m\u001B[43m(\u001B[49m\u001B[43mthread\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mframe\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mevent\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43marg\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43msuspend_type\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mfrom_this_thread\u001B[49m\u001B[43m)\u001B[49m\n",
      "File \u001B[0;32m~/.local/share/JetBrains/Toolbox/apps/pycharm-professional/plugins/python/helpers/pydev/pydevd.py:1199\u001B[0m, in \u001B[0;36mPyDB._do_wait_suspend\u001B[0;34m(self, thread, frame, event, arg, suspend_type, from_this_thread)\u001B[0m\n\u001B[1;32m   1196\u001B[0m             \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_call_mpl_hook()\n\u001B[1;32m   1198\u001B[0m         \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mprocess_internal_commands()\n\u001B[0;32m-> 1199\u001B[0m         \u001B[43mtime\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43msleep\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;241;43m0.01\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[1;32m   1201\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mcancel_async_evaluation(get_current_thread_id(thread), \u001B[38;5;28mstr\u001B[39m(\u001B[38;5;28mid\u001B[39m(frame)))\n\u001B[1;32m   1203\u001B[0m \u001B[38;5;66;03m# process any stepping instructions\u001B[39;00m\n",
      "\u001B[0;31mKeyboardInterrupt\u001B[0m: "
     ]
    }
   ],
   "execution_count": 125
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-21T11:48:12.201926Z",
     "start_time": "2024-05-21T11:48:12.012471Z"
    }
   },
   "cell_type": "code",
   "source": [
    "# load mesa_config.json into a dict:\n",
    "import json\n",
    "import requests\n",
    "config = json.load(open(\"mesa_config.json\"))\n",
    "# send a post request to 127.0.0.1:5000/api/all using the config as the requestbody:\n",
    "\n",
    "\n",
    "def get_mesa_errors_seqs(sequence, error_multiplier=1.0):\n",
    "    def apply_multiplier(config, multiplier):\n",
    "        for err_rule in [\"homopolymer_error_prob\", \"gc_error_prob\"]:\n",
    "            for key in range(len(config[err_rule][\"data\"])):\n",
    "                config[err_rule][\"data\"][key][\"y\"] *= min(100.0, multiplier)\n",
    "        return config\n",
    "    config[\"key\"] = \"IgGD6Cfdlnqa4tUungucZpKp3hfYkt1IDqg0Bn3BxEE\"\n",
    "    config[\"asHTML\"] = False\n",
    "    config[\"sequence\"] = sequence\n",
    "    mesa_config = apply_multiplier(config, error_multiplier)\n",
    "    res = requests.post(\"http://127.0.0.1:5000/api/all\", json=mesa_config)\n",
    "    return res.json()[sequence][\"res\"][\"modified_sequence\"].replace(\" \", \"\")\n",
    "\n",
    "def random_errors(sequences, error_rate=0.013, seq_drop_rate=0.00001):\n",
    "    # apply random errors to the sequences such that the overall per base error rate is error_rate. An error may not lead to the correct base!:\n",
    "    import random\n",
    "    import numpy as np\n",
    "    error_rate = min(1.0, error_rate)\n",
    "    error_rate = max(0.0, error_rate)\n",
    "    out_seqs = []\n",
    "    for seq in sequences:\n",
    "        if random.random() < seq_drop_rate:\n",
    "            continue # dont add the sequence to the output list\n",
    "        for i in range(len(seq)):\n",
    "            if random.random() < error_rate:\n",
    "                mode = np.random.choice([\"sub\", \"ins\", \"del\"], 1, p=[0.8, 0.1, 0.1])[0]\n",
    "                if mode == \"sub\":\n",
    "                    seq = seq[:i] + random.choice(list({\"A\", \"T\", \"G\", \"C\"}.difference(seq[i]))) + seq[i+1:]\n",
    "                elif mode == \"ins\":\n",
    "                    seq = seq[:i] + random.choice(list({\"A\", \"T\", \"G\", \"C\"})) + seq[i:]\n",
    "                else:\n",
    "                    seq = seq[:i] + \" \" + seq[i+1:]\n",
    "        out_seqs.append(seq.replace(\" \",\"\"))\n",
    "    return out_seqs\n",
    "\n",
    "get_mesa_errors_seqs(\"ACACCAGTTGC\")\n",
    "random_errors([\"ACGGCTCGCATACG\",\"AAAAAAAA\"], 0.01, -0.0001)"
   ],
   "id": "ab7f61c611c3b297",
   "outputs": [
    {
     "ename": "JSONDecodeError",
     "evalue": "Expecting value: line 1 column 1 (char 0)",
     "output_type": "error",
     "traceback": [
      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
      "\u001B[0;31mJSONDecodeError\u001B[0m                           Traceback (most recent call last)",
      "File \u001B[0;32m~/Code/OFC4DNA/venv/lib/python3.10/site-packages/requests/models.py:971\u001B[0m, in \u001B[0;36mResponse.json\u001B[0;34m(self, **kwargs)\u001B[0m\n\u001B[1;32m    970\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 971\u001B[0m     \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mcomplexjson\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mloads\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mtext\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    972\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m JSONDecodeError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m    973\u001B[0m     \u001B[38;5;66;03m# Catch JSON-related errors and raise as requests.JSONDecodeError\u001B[39;00m\n\u001B[1;32m    974\u001B[0m     \u001B[38;5;66;03m# This aliases json.JSONDecodeError and simplejson.JSONDecodeError\u001B[39;00m\n",
      "File \u001B[0;32m/usr/lib/python3.10/json/__init__.py:346\u001B[0m, in \u001B[0;36mloads\u001B[0;34m(s, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)\u001B[0m\n\u001B[1;32m    343\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m (\u001B[38;5;28mcls\u001B[39m \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mand\u001B[39;00m object_hook \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mand\u001B[39;00m\n\u001B[1;32m    344\u001B[0m         parse_int \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mand\u001B[39;00m parse_float \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mand\u001B[39;00m\n\u001B[1;32m    345\u001B[0m         parse_constant \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mand\u001B[39;00m object_pairs_hook \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mand\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m kw):\n\u001B[0;32m--> 346\u001B[0m     \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43m_default_decoder\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdecode\u001B[49m\u001B[43m(\u001B[49m\u001B[43ms\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    347\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mcls\u001B[39m \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m:\n",
      "File \u001B[0;32m/usr/lib/python3.10/json/decoder.py:337\u001B[0m, in \u001B[0;36mJSONDecoder.decode\u001B[0;34m(self, s, _w)\u001B[0m\n\u001B[1;32m    333\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"Return the Python representation of ``s`` (a ``str`` instance\u001B[39;00m\n\u001B[1;32m    334\u001B[0m \u001B[38;5;124;03mcontaining a JSON document).\u001B[39;00m\n\u001B[1;32m    335\u001B[0m \n\u001B[1;32m    336\u001B[0m \u001B[38;5;124;03m\"\"\"\u001B[39;00m\n\u001B[0;32m--> 337\u001B[0m obj, end \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mraw_decode\u001B[49m\u001B[43m(\u001B[49m\u001B[43ms\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43midx\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m_w\u001B[49m\u001B[43m(\u001B[49m\u001B[43ms\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m0\u001B[39;49m\u001B[43m)\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mend\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    338\u001B[0m end \u001B[38;5;241m=\u001B[39m _w(s, end)\u001B[38;5;241m.\u001B[39mend()\n",
      "File \u001B[0;32m/usr/lib/python3.10/json/decoder.py:355\u001B[0m, in \u001B[0;36mJSONDecoder.raw_decode\u001B[0;34m(self, s, idx)\u001B[0m\n\u001B[1;32m    354\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mStopIteration\u001B[39;00m \u001B[38;5;28;01mas\u001B[39;00m err:\n\u001B[0;32m--> 355\u001B[0m     \u001B[38;5;28;01mraise\u001B[39;00m JSONDecodeError(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mExpecting value\u001B[39m\u001B[38;5;124m\"\u001B[39m, s, err\u001B[38;5;241m.\u001B[39mvalue) \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m\n\u001B[1;32m    356\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m obj, end\n",
      "\u001B[0;31mJSONDecodeError\u001B[0m: Expecting value: line 1 column 1 (char 0)",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001B[0;31mJSONDecodeError\u001B[0m                           Traceback (most recent call last)",
      "Cell \u001B[0;32mIn[91], line 43\u001B[0m\n\u001B[1;32m     40\u001B[0m         out_seqs\u001B[38;5;241m.\u001B[39mappend(seq\u001B[38;5;241m.\u001B[39mreplace(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m \u001B[39m\u001B[38;5;124m\"\u001B[39m,\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m\"\u001B[39m))\n\u001B[1;32m     41\u001B[0m     \u001B[38;5;28;01mreturn\u001B[39;00m out_seqs\n\u001B[0;32m---> 43\u001B[0m \u001B[43mget_mesa_errors_seqs\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mACACCAGTTGC\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[1;32m     44\u001B[0m random_errors([\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mACGGCTCGCATACG\u001B[39m\u001B[38;5;124m\"\u001B[39m,\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mAAAAAAAA\u001B[39m\u001B[38;5;124m\"\u001B[39m], \u001B[38;5;241m0.01\u001B[39m, \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m0.0001\u001B[39m)\n",
      "Cell \u001B[0;32mIn[91], line 19\u001B[0m, in \u001B[0;36mget_mesa_errors_seqs\u001B[0;34m(sequence, error_multiplier)\u001B[0m\n\u001B[1;32m     17\u001B[0m mesa_config \u001B[38;5;241m=\u001B[39m apply_multiplier(config, error_multiplier)\n\u001B[1;32m     18\u001B[0m res \u001B[38;5;241m=\u001B[39m requests\u001B[38;5;241m.\u001B[39mpost(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mhttp://127.0.0.1:5000/api/all\u001B[39m\u001B[38;5;124m\"\u001B[39m, json\u001B[38;5;241m=\u001B[39mmesa_config)\n\u001B[0;32m---> 19\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mres\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mjson\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m[sequence][\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mres\u001B[39m\u001B[38;5;124m\"\u001B[39m][\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mmodified_sequence\u001B[39m\u001B[38;5;124m\"\u001B[39m]\u001B[38;5;241m.\u001B[39mreplace(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m \u001B[39m\u001B[38;5;124m\"\u001B[39m, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n",
      "File \u001B[0;32m~/Code/OFC4DNA/venv/lib/python3.10/site-packages/requests/models.py:975\u001B[0m, in \u001B[0;36mResponse.json\u001B[0;34m(self, **kwargs)\u001B[0m\n\u001B[1;32m    971\u001B[0m     \u001B[38;5;28;01mreturn\u001B[39;00m complexjson\u001B[38;5;241m.\u001B[39mloads(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mtext, \u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mkwargs)\n\u001B[1;32m    972\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m JSONDecodeError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m    973\u001B[0m     \u001B[38;5;66;03m# Catch JSON-related errors and raise as requests.JSONDecodeError\u001B[39;00m\n\u001B[1;32m    974\u001B[0m     \u001B[38;5;66;03m# This aliases json.JSONDecodeError and simplejson.JSONDecodeError\u001B[39;00m\n\u001B[0;32m--> 975\u001B[0m     \u001B[38;5;28;01mraise\u001B[39;00m RequestsJSONDecodeError(e\u001B[38;5;241m.\u001B[39mmsg, e\u001B[38;5;241m.\u001B[39mdoc, e\u001B[38;5;241m.\u001B[39mpos)\n",
      "\u001B[0;31mJSONDecodeError\u001B[0m: Expecting value: line 1 column 1 (char 0)"
     ]
    }
   ],
   "execution_count": 91
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-21T11:48:13.714234Z",
     "start_time": "2024-05-21T11:48:13.611206Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import random\n",
    "from copy import deepcopy\n",
    "import yaml\n",
    "from time import time\n",
    "\n",
    "\n",
    "def modify_seq(original, pos, probs, results, counter, seqcount, base=None):\n",
    "    pos_sub = []\n",
    "    pos_ins = []\n",
    "    pos_del = []\n",
    "    sub_val = probs[\"substitution\"]\n",
    "    del_val = sub_val + probs[\"deletion\"]\n",
    "    ins_val = del_val + probs[\"insertion\"]\n",
    "    for p in pos:\n",
    "        ran_num = np.random.randint(0, 100)\n",
    "        if ran_num <= sub_val:\n",
    "            pos_sub.append(p)\n",
    "        elif ran_num <= del_val:\n",
    "            pos_del.append(p)\n",
    "        else:\n",
    "            pos_ins.append(p)\n",
    "    #print(pos_sub, pos_del, pos_ins)\n",
    "    results[str(counter)][str(seqcount)][\"sub_pos\"] = pos_sub\n",
    "    results[str(counter)][str(seqcount)][\"ins_pos\"] = pos_ins\n",
    "    results[str(counter)][str(seqcount)][\"del_pos\"] = pos_del\n",
    "    modified = deepcopy(original)\n",
    "    if pos_sub:\n",
    "        modified = substitutions(modified, pos_sub)\n",
    "    if pos_ins:\n",
    "        modified = insertions(modified, pos_ins)\n",
    "    if pos_del:\n",
    "        modified = deletions(modified, pos_del)\n",
    "    return (modified, len(pos_sub), len(pos_ins), len(pos_del))\n",
    "\n",
    "\n",
    "def modify_file(in_path, out_path, probs, results, counter, err_list, weights):\n",
    "    linecount = 0\n",
    "    seqcount = 0\n",
    "    errcount = 0\n",
    "    subcount = 0\n",
    "    inscount = 0\n",
    "    delcount = 0\n",
    "    modseqscount = 0\n",
    "    with open(in_path, \"r\") as inp, open(out_path, \"w\") as out:\n",
    "        while True:\n",
    "            line = inp.readline()\n",
    "            linecount += 1\n",
    "            if not line:\n",
    "                break\n",
    "            if linecount % 2 != 0:\n",
    "                out.write(line)\n",
    "            else:\n",
    "                ori = line.strip()\n",
    "                num_errs = np.random.choice(err_list, 1, p=weights)[0] #p=[0.4, 0.3, 0.2, 0.05, 0.05]\n",
    "                errcount += num_errs\n",
    "                results[str(counter)][str(seqcount)] = dict()\n",
    "                results[str(counter)][str(seqcount)][\"num_errs\"] = int(num_errs)\n",
    "                if not num_errs:\n",
    "                    out.write(line)\n",
    "                else:\n",
    "                    modseqscount += 1\n",
    "                    pos = random.sample(range(0, len(ori)), num_errs)\n",
    "                    results[str(counter)][str(seqcount)][\"error_pos\"] = pos\n",
    "                    seq, nsub, nins, ndels = modify_seq(ori, pos, probs, results, counter, seqcount)\n",
    "                    subcount += nsub\n",
    "                    inscount += nins\n",
    "                    delcount += ndels\n",
    "                    out.write(seq + \"\\n\")\n",
    "            seqcount += 1\n",
    "        results[str(counter)][\"number_of_errors\"] = int(errcount)\n",
    "        results[str(counter)][\"number_of_modified_seqs\"] = int(modseqscount)\n",
    "        results[str(counter)][\"number_of_substitutions\"] = int(subcount)\n",
    "        results[str(counter)][\"number_of_insertions\"] = int(inscount)\n",
    "        results[str(counter)][\"number_of_deletions\"] = int(delcount)\n",
    "\n",
    "def substitutions(original, pos, base=None):\n",
    "    modified = deepcopy(original)\n",
    "    for ele in pos:\n",
    "        if not base:\n",
    "            base = random.choice(list({\"A\", \"T\", \"G\", \"C\"}.difference(original[ele])))\n",
    "        modified = modified[:ele] + base + modified[ele+1:]\n",
    "    return modified\n",
    "\n",
    "\n",
    "def insertions(original, pos, base=None):\n",
    "    modified = deepcopy(original)\n",
    "    shift = 0\n",
    "    pos.sort()\n",
    "    for ele in pos:\n",
    "        if not base:\n",
    "            base = random.choice(list({\"A\", \"T\", \"G\", \"C\"}))\n",
    "        modified = modified[:ele+shift] + base + modified[ele+shift:]\n",
    "        shift += 1\n",
    "    return modified\n",
    "\n",
    "\n",
    "def deletions(original, pos):\n",
    "    modified = deepcopy(original)\n",
    "    shift = 0\n",
    "    pos.sort()\n",
    "    for ele in pos:\n",
    "        modified = modified[:ele-shift] + modified[ele-shift+1:]\n",
    "    return modified\n",
    "\n",
    "\n",
    "in_folder = \"clusts/\"\n",
    "in_file = \"cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta\"\n",
    "in_path = f\"{in_folder}{in_file}\"\n",
    "out_path = f\"{in_folder}error_test/{in_file}\"\n",
    "length = 116\n",
    "probs = {\"substitution\": 80, \"insertion\": 10, \"deletion\": 10}\n",
    "err_list = [0, 1, 2, 3, 4, 5, 6, 7]\n",
    "weights = [0.15, 0.15, 0.25, 0.2, 0.1, 0.06, 0.05, 0.04] #weights = [0.35, 0.25, 0.15, 0.15, 0.05, 0.03, 0.01, 0.01]\n",
    "iterations = 1\n",
    "results = dict()\n",
    "results[\"params\"] = dict()\n",
    "results[\"params\"][\"err_type\"] = probs\n",
    "results[\"params\"][\"num_errs\"] = err_list\n",
    "results[\"params\"][\"errs_weights\"] = weights\n",
    "counter = 0\n",
    "results[str(counter)] = dict()\n",
    "print(\"start\")\n",
    "start = time()\n",
    "modify_file(in_path, out_path, probs, results, counter, err_list, weights)\n",
    "end = time()\n",
    "print(end - start)\n",
    "with open(\"test_split.yaml\", \"w\") as o_:\n",
    "    yaml.dump(results, o_)"
   ],
   "id": "5f8ed102ed761803",
   "outputs": [
    {
     "ename": "FileNotFoundError",
     "evalue": "[Errno 2] No such file or directory: 'clusts/error_test/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta'",
     "output_type": "error",
     "traceback": [
      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
      "\u001B[0;31mFileNotFoundError\u001B[0m                         Traceback (most recent call last)",
      "Cell \u001B[0;32mIn[92], line 124\u001B[0m\n\u001B[1;32m    122\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mstart\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m    123\u001B[0m start \u001B[38;5;241m=\u001B[39m time()\n\u001B[0;32m--> 124\u001B[0m \u001B[43mmodify_file\u001B[49m\u001B[43m(\u001B[49m\u001B[43min_path\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mout_path\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mprobs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mresults\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mcounter\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43merr_list\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mweights\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    125\u001B[0m end \u001B[38;5;241m=\u001B[39m time()\n\u001B[1;32m    126\u001B[0m \u001B[38;5;28mprint\u001B[39m(end \u001B[38;5;241m-\u001B[39m start)\n",
      "Cell \u001B[0;32mIn[92], line 44\u001B[0m, in \u001B[0;36mmodify_file\u001B[0;34m(in_path, out_path, probs, results, counter, err_list, weights)\u001B[0m\n\u001B[1;32m     42\u001B[0m delcount \u001B[38;5;241m=\u001B[39m \u001B[38;5;241m0\u001B[39m\n\u001B[1;32m     43\u001B[0m modseqscount \u001B[38;5;241m=\u001B[39m \u001B[38;5;241m0\u001B[39m\n\u001B[0;32m---> 44\u001B[0m \u001B[38;5;28;01mwith\u001B[39;00m \u001B[38;5;28mopen\u001B[39m(in_path, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mr\u001B[39m\u001B[38;5;124m\"\u001B[39m) \u001B[38;5;28;01mas\u001B[39;00m inp, \u001B[38;5;28;43mopen\u001B[39;49m\u001B[43m(\u001B[49m\u001B[43mout_path\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mw\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m)\u001B[49m \u001B[38;5;28;01mas\u001B[39;00m out:\n\u001B[1;32m     45\u001B[0m     \u001B[38;5;28;01mwhile\u001B[39;00m \u001B[38;5;28;01mTrue\u001B[39;00m:\n\u001B[1;32m     46\u001B[0m         line \u001B[38;5;241m=\u001B[39m inp\u001B[38;5;241m.\u001B[39mreadline()\n",
      "File \u001B[0;32m~/Code/OFC4DNA/venv/lib/python3.10/site-packages/IPython/core/interactiveshell.py:310\u001B[0m, in \u001B[0;36m_modified_open\u001B[0;34m(file, *args, **kwargs)\u001B[0m\n\u001B[1;32m    303\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m file \u001B[38;5;129;01min\u001B[39;00m {\u001B[38;5;241m0\u001B[39m, \u001B[38;5;241m1\u001B[39m, \u001B[38;5;241m2\u001B[39m}:\n\u001B[1;32m    304\u001B[0m     \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mValueError\u001B[39;00m(\n\u001B[1;32m    305\u001B[0m         \u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mIPython won\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mt let you open fd=\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mfile\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m by default \u001B[39m\u001B[38;5;124m\"\u001B[39m\n\u001B[1;32m    306\u001B[0m         \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mas it is likely to crash IPython. If you know what you are doing, \u001B[39m\u001B[38;5;124m\"\u001B[39m\n\u001B[1;32m    307\u001B[0m         \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124myou can use builtins\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m open.\u001B[39m\u001B[38;5;124m\"\u001B[39m\n\u001B[1;32m    308\u001B[0m     )\n\u001B[0;32m--> 310\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mio_open\u001B[49m\u001B[43m(\u001B[49m\u001B[43mfile\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43margs\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[38;5;241;43m*\u001B[39;49m\u001B[43mkwargs\u001B[49m\u001B[43m)\u001B[49m\n",
      "\u001B[0;31mFileNotFoundError\u001B[0m: [Errno 2] No such file or directory: 'clusts/error_test/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta'"
     ]
    }
   ],
   "execution_count": 92
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-21T11:48:27.656672Z",
     "start_time": "2024-05-21T11:48:14.452520Z"
    }
   },
   "cell_type": "code",
   "outputs": [],
   "execution_count": 93,
   "source": [
    "from NOREC4DNA.invivo_window_decoder import load_fasta\n",
    "\n",
    "files = glob.glob(\"clusts/cs_23_I_max_2_hp_10_gc_*.fasta\")\n",
    "files.append(\"clusts/sleeping_beauty_grass.fasta\")\n",
    "files.append(\"clusts/sleeping_beauty_dna_fountain_cs23.fasta\")\n",
    "\n",
    "grass_enc = load_fasta(\"clusts/sleeping_beauty_grass.fasta\")\n",
    "# calculate the length of the sequences:\n",
    "length = \"\".join(list(grass_enc.values())).replace(\"\\n\", \"\").replace(\"\\r\", \"\").replace(\" \", \"\")\n",
    "\n",
    "for error_rate in [0.01, 0.02, 0.03, 0.04, 0.05]:\n",
    "    # iterate over all files in \"files\" and add mutations to the sequences:\n",
    "    for file in files:\n",
    "        # load file as a fasta file:\n",
    "        total_nts = 0\n",
    "        out = {}\n",
    "        seqs = load_fasta(file)\n",
    "        for key, value in seqs.items():\n",
    "            total_nts += len(value)\n",
    "            out[key] = random_errors([file], 0.013, 0.00001)\n",
    "            if total_nts >= len(length):\n",
    "                # ensure we only use as much sequence as the grass code produced!\n",
    "                break\n",
    "        # save the sequences to a new file:\n",
    "        with open(f\"clusts/error/{file.replace('clusts/', '')}_error_{error_rate}.fasta\", \"w\") as o_:\n",
    "            for key, value in out.items():\n",
    "                o_.write(f\">{key}\\n\")\n",
    "                o_.write(f\"{value}\\n\")"
   ],
   "id": "36055046e41f7103"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-21T13:05:56.235895Z",
     "start_time": "2024-05-21T13:04:38.788429Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import os\n",
    "import base64\n",
    "number_of_chunks = 289  # or 191?\n",
    "\n",
    "files = glob.glob(\"clusts/error/cs_23_I_max_2_hp_10_gc_*.fasta\")\n",
    "\n",
    "csv_line = \"file,dist_name,use_payload_xor,seed_spacing,static_number_of_chunks,error_rate,success,decoded_data\\n\"\n",
    "\n",
    "for file in files:\n",
    "    error_correction = get_error_correction_decode(\"reedsolomon\", 2)\n",
    "    dist, dist_name = get_dist(file)\n",
    "    use_payload_xor = get_payload_xor(file)\n",
    "    seed_spacing = get_seed_spacing(file)\n",
    "    static_number_of_chunks = number_of_chunks\n",
    "    error_rate = float(file.split(\"error_\")[1].split(\".fasta\")[0])\n",
    "    print(f\"Current file and settings: {file}, {dist}, {use_payload_xor}, {seed_spacing}, {static_number_of_chunks}\")\n",
    "    #try:\n",
    "    try:\n",
    "        res = decode_from_fasta(file, number_of_chunks=number_of_chunks, dist=dist, error_correction=error_correction,\n",
    "                                use_seed_xor=True, use_payload_xor=use_payload_xor, seed_spacing=seed_spacing,\n",
    "                                use_headerchunk=False)\n",
    "    except Exception as e:\n",
    "        res = (False, \"\")\n",
    "        raise e\n",
    "    csv_line += f\"{file},{dist_name},{use_payload_xor},{seed_spacing},{static_number_of_chunks},{error_rate},{res[0]},{base64.b64encode(res[1].encode())}\\n\"\n",
    "    \n",
    "with open(\"clusts/error/error_results.csv\", \"w\") as o_:\n",
    "    o_.write(csv_line)\n",
    "        \n",
    "    #except Exception as e:\n",
    "    #    continue"
   ],
   "id": "e54c5b5617c7c19a",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Could not decode Chunk 287\n",
      "Could not decode Chunk 288\n",
      "Decoded Packets: 290\n",
      "Corrupt Packets : 0\n",
      "Success: True\n",
      "Saved file as 'DEC_out_file.fasta'\n",
      "<xml><var name=\"_dummy_ret_val\"  />\n",
      "<var name=\"_dummy_ipython_val\"  />\n",
      "<var name=\"_dummy_special_var\"  />\n",
      "<var name=\"RU10Encoder\" type=\"ABCMeta\" qualifier=\"abc\" value=\"%3Cclass %27NOREC4DNA.norec4dna.RU10Encoder.RU10Encoder%27&gt;\" isContainer=\"True\" />\n",
      "<var name=\"__py_debug_temp_var_1001208864\" type=\"int\" qualifier=\"builtins\" value=\"27\" />\n",
      "<var name=\"asdf\" type=\"list\" qualifier=\"builtins\" value=\"%5B%3C used_packets%3A %5B23%2C 300%5D %2C Data%3A %5B104 115  99  51  26  18  29 116  88  60   8  55 153 192 139 231 216 206%0A  20  50   0  52  18%5D &gt;%5D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"ax\" type=\"Axes\" qualifier=\"matplotlib.axes._axes\" value=\"%3CAxes%3A title=%7B%27center%27%3A %27Minimum free energy %28MFE%29 of the generated sequences%27%7D%2C xlabel=%27dna fountain %27&gt;\" isContainer=\"True\" />\n",
      "<var name=\"bmp_low_entropy_diff_dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.            1136.9807546     9091.20111762   12111.88508948%2C   13017.1708098    57959.04100808   71798.24459634   72487.1842063%2C  125647.56019394  167454.99443843  207887.59917079  253583.4801622%2C  261718.31786311  310984.9412345   321695.14945959  368816.37254484%2C  393617.58142113  398484.87252954  446229.27315371  469314.84015955%2C  477620.72923345  482476.68746324  520877.86792584  523718.64231146%2C  567701.29582963  591072.50115539  612037.48997345  628878.87686348%2C  681353.80436257  722346.76126439  770935.25023072  793475.63495812%2C  803332.69084969  847730.75224056  851048.79037268  874467.13097433%2C  903439.69486354  922022.95754105  977234.39739524 1022344.39518796%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"bmp_low_entropy_evo_dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.               0.               0.               0.%2C       0.               0.               0.               0.%2C       0.            5213.34222692   27397.06087366   27397.06087366%2C   27397.06087366   76259.50656745  118731.99703658  118731.99703658%2C  169159.02505416  169159.02505416  169159.02505416  241778.6531302%2C  289301.16954725  289301.16954725  289301.16954725  334042.455604%2C  334042.455604    395036.41601383  428516.1901104   468383.31221304%2C  515536.16651901  552849.46749891  584038.85877362  637743.13880125%2C  677025.87781114  715277.21144298  765344.2744503   822771.30012886%2C  870256.00307536  951876.06719783  995543.61290259 1031900.06437448%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"conf_name\" type=\"str\" qualifier=\"builtins\" value=\"sleeping_beauty_dna_fountain_cs23.fasta\" />\n",
      "<var name=\"config\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%27acgt_only%27%3A True%2C %27asHTML%27%3A False%2C %27do_max_expect%27%3A False%2C %27email%27%3A %27%27%2C %27enabledUndesiredSeqs%27%3A %5B%7B%27description%27%3A %27Lox site spacer loxP WT https%3A//doi.org/10.1007/978-981-10-3874-733%27%2C %27enabled%27%3A True%2C %27error_prob%27%3A %27100.0%27%2C %27sequence%27%3A %27GCATACAT%27%7D%2C %7B%27description%27%3A %27Lox site spacer lox1 https%3A//doi.org/10.1186/1471-2164-7-73%27%2C %27enabled%27%3A True%2C %27error_prob%27%3A %27100.0%27%2C %27sequence%27%3A %27TGGTATTA%27%7D%2C %7B%27description%27%3A %27Lox site spacer lox2 https%3A//doi.org/10.1186/1471-2164-7-73%27%2C %27enabled%27%3A True%2C %27error_prob%27%3A %27100.0%27%2C %27sequence%27%3A %27TTCTATCT%27%7D%2C %7B%27description%27%3A %27Lox site spacer lox3 https%3A//doi.org/10.1186/1471-2164-7-73%27%2C %27enabled%27%3A True%2C %27error_prob%27%3A %27100.0%27%2C %27sequence%27%3A %27GGATACTT%27%7D%5D%2C %27err_simulation_order%27%3A %7B%27Sequencing%27%3A %5B%7B%27conf%27%3A %7B%27err_attributes%27%3A %7B%27deletion%27%3A %7B...%7D%2C %27insertion%27%3A %7B...%7D%2C %27mismatch%27%3A %7B...%7D%7D%2C %27err_data%27%3A %7B%27deletion%27%3A 0.0018%2C %27insertion%27%3A 0.0011%2C %27mismatch%27%3A 0.79%2C %27raw_rate%27%3A 0.0032%7D%2C %27type%27%3A %27sequencing%27%7D%2C %27cycles%27%3A 1%2C %27id%27%3A %2736%27%2C %27name%27%3A %27Paired End%27%7D%5D%2C %27Storage/PCR%27%3A %5B%7B%27conf%27...\" isContainer=\"True\" shape=\"20\" />\n",
      "<var name=\"counter\" type=\"int\" qualifier=\"builtins\" value=\"0\" />\n",
      "<var name=\"csv_line\" type=\"str\" qualifier=\"builtins\" value=\"file%2Cdist_name%2Cuse_payload_xor%2Cseed_spacing%2Cstatic_number_of_chunks%2Cerror_rate%2Csuccess%2Cdecoded_data%0A\" />\n",
      "<var name=\"df\" type=\"DataFrame\" qualifier=\"pandas.core.frame\" value=\"%5B%27file%27%2C %27dist_name%27%2C %27use_payload_xor%27%2C %27seed_spacing%27%2C %27static_number_of_chunks%27%2C %27error_rate%27%2C %27success%27%2C %27decoded_data%27%5D %5B0    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   %5D %5B1    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...   evo_compress_encrypt   %5D %5B2    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...  diff_compress_encrypt   %5D %5B3    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   %5D %5B4    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   %5D %5B..                                                 ...                    ...   %5D %5B145  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...       low_entropy_diff   %5D %5B146  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...       low_entropy_diff   %5D %5B147  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...                 raptor   %5D %5B148  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...  diff_compress_encrypt   %5D %5B149  clusts/error/cs_23_I_max_2_hp_10_gc_opt...\" isContainer=\"True\" shape=\"(150, 8)\" />\n",
      "<var name=\"diff_compress_encrypt_high_entropy_dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.               0.           29089.79521874   72481.36996913%2C   98340.54009726  131567.39732824  176222.33645313  228831.95105282%2C  252326.29538902  276175.72445691  299450.09035552  299450.09035552%2C  325747.79207801  350286.21356139  387420.63799373  393380.85543471%2C  438114.97705523  443148.86850801  465291.78684474  507620.53436244%2C  554815.62818098  565762.61188028  587194.87535876  631723.17658683%2C  631723.17658683  651761.53608897  680773.99454248  709201.30476058%2C  744801.68917068  762349.30565287  779814.00716521  785066.34697717%2C  829065.08323761  838672.95527928  858778.80081104  886807.58531494%2C  901742.19919218  922968.09448734  952513.50238877  980596.6076461%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.               0.               0.               0.%2C       0.               0.               0.               0.%2C       0.            5213.34222692   27397.06087366   27397.06087366%2C   27397.06087366   76259.50656745  118731.99703658  118731.99703658%2C  169159.02505416  169159.02505416  169159.02505416  241778.6531302%2C  289301.16954725  289301.16954725  289301.16954725  334042.455604%2C  334042.455604    395036.41601383  428516.1901104   468383.31221304%2C  515536.16651901  552849.46749891  584038.85877362  637743.13880125%2C  677025.87781114  715277.21144298  765344.2744503   822771.30012886%2C  870256.00307536  951876.06719783  995543.61290259 1031900.06437448%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"dist_name\" type=\"str\" qualifier=\"builtins\" value=\"low_entropy_evo\" />\n",
      "<var name=\"encoder\" type=\"RU10Encoder\" qualifier=\"NOREC4DNA.norec4dna.RU10Encoder\" value=\"%3CNOREC4DNA.norec4dna.RU10Encoder.RU10Encoder object at 0x7fea648a58a0&gt;\" isContainer=\"True\" />\n",
      "<var name=\"err_list\" type=\"list\" qualifier=\"builtins\" value=\"%5B0%2C 1%2C 2%2C 3%2C 4%2C 5%2C 6%2C 7%5D\" isContainer=\"True\" shape=\"8\" />\n",
      "<var name=\"error_rate\" type=\"float\" qualifier=\"builtins\" value=\"0.05\" />\n",
      "<var name=\"evo_compress_encrypt_high_entropy_dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.            1425.43934062   27002.90907888   43690.73327553%2C   63294.81537234   87788.17204801  121728.30753776  140829.34227724%2C  180834.71376757  208373.25073121  236445.45271099  259943.84686175%2C  290359.40640509  321260.12229916  354279.35337277  382179.33996018%2C  413629.67619777  442249.90271307  469765.28196638  500719.78465128%2C  533697.05550466  561652.23810626  561652.23810626  600011.35261877%2C  624152.76490294  654704.19114975  697183.48788851  724376.2883197%2C  751004.84422912  771229.47574536  797325.55293154  823503.60307259%2C  854062.55679468  890863.07690872  910159.55153303  938570.27144896%2C  963145.65800847  979819.7521839  1013685.83134719 1043822.30710253%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"fig\" type=\"Figure\" qualifier=\"matplotlib.figure\" value=\"%3CFigure size 640x480 with 1 Axes&gt;\" isContainer=\"True\" />\n",
      "<var name=\"file\" type=\"str\" qualifier=\"builtins\" value=\"clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing2_payloadxor.fasta_error_0.05.fasta\" />\n",
      "<var name=\"files\" type=\"list\" qualifier=\"builtins\" value=\"%5B%27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing2_payloadxor.fasta_error_0.05.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_evo_compress_encrypt_high_entropy_dist_seedspacing2.fasta_error_0.01.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_diff_compress_encrypt_high_entropy_dist_seedspacing2.fasta_error_0.05.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing4_payloadxor.fasta_error_0.01.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing2.fasta_error_0.01.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_evo_compress_encrypt_high_entropy_dist_seedspacing2_payloadxor.fasta_error_0.03.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing4.fasta_error_0.03.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_diff_compres...\" isContainer=\"True\" shape=\"150\" />\n",
      "<var name=\"grass_enc\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%270%27%3A %27CGCCCGATACTCCACGAGACAACAACACATACAATAGACGCAGAGACGATACCGAATCTGGGTGCGGTCGTGGTGGTCGCGGACCTATGCACGCGTGACCATAATTCGCCGGAGCGA%27%2C %271%27%3A %27CGACTACCGCATATGAAGCCAACAACAGGTACTAACCACAGACGTCGTTAGGAGCCGCCATGAACTCGTGTGGATGTACAGTCACTCCAGAATGGCAACCTCCCGAGCATGTAGCCG%27%2C %2710%27%3A %27TTATCTGAGGAGCCTATAGTAACAACAATCCACCACAGTCTGCGTAGCCTATAGGTACTGGGTGGACCAAGCAGTCGTGATGCGCCACCATATGACTTAACTATAGAGCGACATGTA%27%2C %27100%27%3A %27GGCTACCCTGACATACGCGGAGCAACAGTAGGTCGTTGAAATTTGCCACTAGCAAACACGTAGGCTCTGCATCCAGTCCTCCGCTCGTGAATCCCAGCTCTCCTGTACGCTCGTCAT%27%2C %27101%27%3A %27CTCTGAACACGACCTCGTTGAGCAACAGGAACGATCTCTGGTCACCTCAGTTTAGTCCCAGGCTACGTACGTTCTGGACAGTTGCACAAGACTTGACCGGTCGTCTAGTCAGAGGGA%27%2C %27102%27%3A %27GGCAAGACGGAGGAGGAGATAGCAACATCTGGATATGTCGCATTGAATCACGTCGCAAACGAGGAGGTACCACCTAGTGTAGCTGCAGGTCCAGCATATCCATTGACACTCCAGCAT%27%2C %27103%27%3A %27TTAAACCGTAACATGTGACTAGCAACACACAGAAAGACTCCACTCTTATTGGGTGTACTGAATCCTCGTGCTCATTAGCTGTCGTTGCTCTGAGTGCCGATCATCCCATTGGACCGC%27%2C %27104%27%3A %27GTCCGTGAGGACAGTTATGTAGCAACACGATCGTTAGTCCCTTCGAGAGCATGCGATTCGCCAAATACAGGCCCGCGATTACTGGGAGCTCCGGATGCTA...\" isContainer=\"True\" shape=\"713\" />\n",
      "<var name=\"in_file\" type=\"str\" qualifier=\"builtins\" value=\"cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta\" />\n",
      "<var name=\"in_folder\" type=\"str\" qualifier=\"builtins\" value=\"clusts/\" />\n",
      "<var name=\"in_path\" type=\"str\" qualifier=\"builtins\" value=\"clusts/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta\" />\n",
      "<var name=\"intermediate_symbols\" type=\"_lru_cache_wrapper\" qualifier=\"functools\" value=\"%3Cfunctools._lru_cache_wrapper object at 0x7fea85a7e610&gt;\" isContainer=\"True\" />\n",
      "<var name=\"iterations\" type=\"int\" qualifier=\"builtins\" value=\"1\" />\n",
      "<var name=\"key\" type=\"str\" qualifier=\"builtins\" value=\"packet\" />\n",
      "<var name=\"key_title\" type=\"str\" qualifier=\"builtins\" value=\"dna fountain \" />\n",
      "<var name=\"length\" type=\"str\" qualifier=\"builtins\" value=\"CGCCCGATACTCCACGAGACAACAACACATACAATAGACGCAGAGACGATACCGAATCTGGGTGCGGTCGTGGTGGTCGCGGACCTATGCACGCGTGACCATAATTCGCCGGAGCGACGACTACCGCATATGAAGCCAACAACAGGTACTAACCACAGACGTCGTTAGGAGCCGCCATGAACTCGTGTGGATGTACAGTCACTCCAGAATGGCAACCTCCCGAGCATGTAGCCGACGCGCCGAAACCAGAAGGCAA\" />\n",
      "<var name=\"number_of_chunks\" type=\"int\" qualifier=\"builtins\" value=\"289\" />\n",
      "<var name=\"o_\" type=\"TextIOWrapper\" qualifier=\"_io\" value=\"%3C_io.TextIOWrapper name=%27clusts/error/error_results.csv%27 mode=%27w%27 encoding=%27UTF-8%27&gt;\" isContainer=\"True\" />\n",
      "<var name=\"out\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%27packet%27%3A %5B%27clusts/sleeping_Teauty_dna_fountain_cs23.fasta%27%5D%7D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"out_path\" type=\"str\" qualifier=\"builtins\" value=\"clusts/error_test/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta\" />\n",
      "<var name=\"probs\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%27deletion%27%3A 10%2C %27insertion%27%3A 10%2C %27substitution%27%3A 80%7D\" isContainer=\"True\" shape=\"3\" />\n",
      "<var name=\"raptor_dist\" type=\"list\" qualifier=\"builtins\" value=\"%5B0%2C 10241%2C 491582%2C 712794%2C 831695%2C 831695%2C 831695%2C 831695%2C 831695%2C 831695%2C 948446%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1048576%5D\" isContainer=\"True\" shape=\"41\" />\n",
      "<var name=\"res\" type=\"tuple\" qualifier=\"builtins\" value=\"%28False%2C %27%27%29\" isContainer=\"True\" shape=\"2\" />\n",
      "<var name=\"results\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%270%27%3A %7B%7D%2C %27params%27%3A %7B%27err_type%27%3A %7B%27deletion%27%3A 10%2C %27insertion%27%3A 10%2C %27substitution%27%3A 80%7D%2C %27errs_weights%27%3A %5B0.15%2C 0.15%2C 0.25%2C 0.2%2C 0.1%2C 0.06%2C 0.05%2C 0.04%5D%2C %27num_errs%27%3A %5B0%2C 1%2C 2%2C 3%2C 4%2C 5%2C 6%2C 7%5D%7D%7D\" isContainer=\"True\" shape=\"2\" />\n",
      "<var name=\"seed_spacing\" type=\"int\" qualifier=\"builtins\" value=\"2\" />\n",
      "<var name=\"seqs\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%27packet%27%3A %27CCACCCGTGACTGTGTAGCTACTACGTCCCACAATAAAGAAATCCGTAACAGCCAGAAGCCCAGCACTACATCCCTCAGTCACGAAATCATGGCCTTTCCGTTACATTATTAGGAC%27%7D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"start\" type=\"float\" qualifier=\"builtins\" value=\"1716292093.6295974\" />\n",
      "<var name=\"static_number_of_chunks\" type=\"int\" qualifier=\"builtins\" value=\"289\" />\n",
      "<var name=\"time\" type=\"builtin_function_or_method\" qualifier=\"builtins\" value=\"%3Cbuilt-in function time&gt;\" isContainer=\"True\" />\n",
      "<var name=\"total_nts\" type=\"int\" qualifier=\"builtins\" value=\"116\" />\n",
      "<var name=\"use_payload_xor\" type=\"bool\" qualifier=\"builtins\" value=\"True\" />\n",
      "<var name=\"value\" type=\"list\" qualifier=\"builtins\" value=\"%5B%27clusts/sleeping_Teauty_dna_fountain_cs23.fasta%27%5D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"weights\" type=\"list\" qualifier=\"builtins\" value=\"%5B0.15%2C 0.15%2C 0.25%2C 0.2%2C 0.1%2C 0.06%2C 0.05%2C 0.04%5D\" isContainer=\"True\" shape=\"8\" />\n",
      "</xml>\n",
      "Current file and settings: clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing2_payloadxor.fasta_error_0.05.fasta, [      0.               0.               0.               0.\n",
      "       0.               0.               0.               0.\n",
      "       0.            5213.34222692   27397.06087366   27397.06087366\n",
      "   27397.06087366   76259.50656745  118731.99703658  118731.99703658\n",
      "  169159.02505416  169159.02505416  169159.02505416  241778.6531302\n",
      "  289301.16954725  289301.16954725  289301.16954725  334042.455604\n",
      "  334042.455604    395036.41601383  428516.1901104   468383.31221304\n",
      "  515536.16651901  552849.46749891  584038.85877362  637743.13880125\n",
      "  677025.87781114  715277.21144298  765344.2744503   822771.30012886\n",
      "  870256.00307536  951876.06719783  995543.61290259 1031900.06437448\n",
      " 1048576.        ], True, 2, 289\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "ename": "AttributeError",
     "evalue": "'NoneType' object has no attribute 'isPotentionallySolvable'",
     "output_type": "error",
     "traceback": [
      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
      "\u001B[0;31mAttributeError\u001B[0m                            Traceback (most recent call last)",
      "Cell \u001B[0;32mIn[123], line 24\u001B[0m\n\u001B[1;32m     22\u001B[0m     \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m     23\u001B[0m         res \u001B[38;5;241m=\u001B[39m (\u001B[38;5;28;01mFalse\u001B[39;00m, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[0;32m---> 24\u001B[0m         \u001B[38;5;28;01mraise\u001B[39;00m e\n\u001B[1;32m     25\u001B[0m     csv_line \u001B[38;5;241m+\u001B[39m\u001B[38;5;241m=\u001B[39m \u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mfile\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m,\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mdist_name\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m,\u001B[39m\u001B[38;5;132;01m{\u001B[39;00muse_payload_xor\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m,\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mseed_spacing\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m,\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mstatic_number_of_chunks\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m,\u001B[39m\u001B[38;5;132;01m{\u001B[39;00merror_rate\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m,\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mres[\u001B[38;5;241m0\u001B[39m]\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m,\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mbase64\u001B[38;5;241m.\u001B[39mb64encode(res[\u001B[38;5;241m1\u001B[39m]\u001B[38;5;241m.\u001B[39mencode())\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;130;01m\\n\u001B[39;00m\u001B[38;5;124m\"\u001B[39m\n\u001B[1;32m     27\u001B[0m \u001B[38;5;28;01mwith\u001B[39;00m \u001B[38;5;28mopen\u001B[39m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mclusts/error/error_results.csv\u001B[39m\u001B[38;5;124m\"\u001B[39m, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mw\u001B[39m\u001B[38;5;124m\"\u001B[39m) \u001B[38;5;28;01mas\u001B[39;00m o_:\n",
      "Cell \u001B[0;32mIn[123], line 19\u001B[0m\n\u001B[1;32m     17\u001B[0m \u001B[38;5;66;03m#try:\u001B[39;00m\n\u001B[1;32m     18\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m---> 19\u001B[0m     res \u001B[38;5;241m=\u001B[39m \u001B[43mdecode_from_fasta\u001B[49m\u001B[43m(\u001B[49m\u001B[43mfile\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mnumber_of_chunks\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mnumber_of_chunks\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mdist\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mdist\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43merror_correction\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43merror_correction\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m     20\u001B[0m \u001B[43m                            \u001B[49m\u001B[43muse_seed_xor\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mTrue\u001B[39;49;00m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43muse_payload_xor\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43muse_payload_xor\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mseed_spacing\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mseed_spacing\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m     21\u001B[0m \u001B[43m                            \u001B[49m\u001B[43muse_headerchunk\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m)\u001B[49m\n\u001B[1;32m     22\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m     23\u001B[0m     res \u001B[38;5;241m=\u001B[39m (\u001B[38;5;28;01mFalse\u001B[39;00m, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n",
      "Cell \u001B[0;32mIn[122], line 32\u001B[0m, in \u001B[0;36mdecode_from_fasta\u001B[0;34m(filename, number_of_chunks, dist, error_correction, use_seed_xor, use_payload_xor, seed_spacing, use_headerchunk)\u001B[0m\n\u001B[1;32m     30\u001B[0m decoder\u001B[38;5;241m.\u001B[39mcreateAuxBlocks()\n\u001B[1;32m     31\u001B[0m decoder\u001B[38;5;241m.\u001B[39mprogress_bar \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39mcreate_progress_bar(number_of_chunks \u001B[38;5;241m+\u001B[39m \u001B[38;5;241m0.02\u001B[39m \u001B[38;5;241m*\u001B[39m number_of_chunks)\n\u001B[0;32m---> 32\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[43mdecoder\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdecodeFile\u001B[49m\u001B[43m(\u001B[49m\u001B[43mid_len_format\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mI\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[1;32m     33\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mSuccess: \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mres\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m     34\u001B[0m res_data \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39msaveDecodedFile(last_chunk_len_format\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m\"\u001B[39m, null_is_terminator\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mFalse\u001B[39;00m, print_to_output\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mFalse\u001B[39;00m,\n\u001B[1;32m     35\u001B[0m                         partial_decoding\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mTrue\u001B[39;00m)\n",
      "File \u001B[0;32m~/Code/OFC4DNA/NOREC4DNA/norec4dna/RU10Decoder.py:270\u001B[0m, in \u001B[0;36mRU10Decoder.decodeFile\u001B[0;34m(self, packet_len_format, crc_len_format, number_of_chunks_len_format, id_len_format)\u001B[0m\n\u001B[1;32m    268\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mDecoded Packets: \u001B[39m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;241m+\u001B[39m \u001B[38;5;28mstr\u001B[39m(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mcorrect))\n\u001B[1;32m    269\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mCorrupt Packets : \u001B[39m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;241m+\u001B[39m \u001B[38;5;28mstr\u001B[39m(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mcorrupt))\n\u001B[0;32m--> 270\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mGEPP\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43misPotentionallySolvable\u001B[49m() \u001B[38;5;129;01mand\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mread_all_before_decode:\n\u001B[1;32m    271\u001B[0m     decoded \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mGEPP\u001B[38;5;241m.\u001B[39msolve()\n\u001B[1;32m    272\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m decoded \u001B[38;5;129;01mand\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mEOF:\n",
      "\u001B[0;31mAttributeError\u001B[0m: 'NoneType' object has no attribute 'isPotentionallySolvable'"
     ]
    }
   ],
   "execution_count": 123
  },
  {
   "cell_type": "code",
   "outputs": [
    {
     "data": {
      "text/plain": "                                                  file              dist_name  \\\n0    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   \n1    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...   evo_compress_encrypt   \n2    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...  diff_compress_encrypt   \n3    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   \n4    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   \n..                                                 ...                    ...   \n145  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...       low_entropy_diff   \n146  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...       low_entropy_diff   \n147  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...                 raptor   \n148  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...  diff_compress_encrypt   \n149  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   \n\n     use_payload_xor  seed_spacing  static_number_of_chunks  error_rate  \\\n0               True             2                      289        0.05   \n1              False             2                      289        0.01   \n2              False             2                      289        0.05   \n3               True             4                      289        0.01   \n4              False             2                      289        0.01   \n..               ...           ...                      ...         ...   \n145            False             4                      289        0.01   \n146            False             2                      289        0.02   \n147            False             2                      289        0.01   \n148            False             4                      289        0.05   \n149            False             4                      289        0.05   \n\n     success decoded_data  \n0      False          b''  \n1      False          b''  \n2      False          b''  \n3      False          b''  \n4      False          b''  \n..       ...          ...  \n145    False          b''  \n146    False          b''  \n147    False          b''  \n148    False          b''  \n149    False          b''  \n\n[150 rows x 8 columns]",
      "text/html": "<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>file</th>\n      <th>dist_name</th>\n      <th>use_payload_xor</th>\n      <th>seed_spacing</th>\n      <th>static_number_of_chunks</th>\n      <th>error_rate</th>\n      <th>success</th>\n      <th>decoded_data</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>0</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>low_entropy_evo</td>\n      <td>True</td>\n      <td>2</td>\n      <td>289</td>\n      <td>0.05</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>1</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>evo_compress_encrypt</td>\n      <td>False</td>\n      <td>2</td>\n      <td>289</td>\n      <td>0.01</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>2</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>diff_compress_encrypt</td>\n      <td>False</td>\n      <td>2</td>\n      <td>289</td>\n      <td>0.05</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>3</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>low_entropy_evo</td>\n      <td>True</td>\n      <td>4</td>\n      <td>289</td>\n      <td>0.01</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>4</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>low_entropy_evo</td>\n      <td>False</td>\n      <td>2</td>\n      <td>289</td>\n      <td>0.01</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>...</th>\n      <td>...</td>\n      <td>...</td>\n      <td>...</td>\n      <td>...</td>\n      <td>...</td>\n      <td>...</td>\n      <td>...</td>\n      <td>...</td>\n    </tr>\n    <tr>\n      <th>145</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>low_entropy_diff</td>\n      <td>False</td>\n      <td>4</td>\n      <td>289</td>\n      <td>0.01</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>146</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>low_entropy_diff</td>\n      <td>False</td>\n      <td>2</td>\n      <td>289</td>\n      <td>0.02</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>147</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>raptor</td>\n      <td>False</td>\n      <td>2</td>\n      <td>289</td>\n      <td>0.01</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>148</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>diff_compress_encrypt</td>\n      <td>False</td>\n      <td>4</td>\n      <td>289</td>\n      <td>0.05</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n    <tr>\n      <th>149</th>\n      <td>clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...</td>\n      <td>low_entropy_evo</td>\n      <td>False</td>\n      <td>4</td>\n      <td>289</td>\n      <td>0.05</td>\n      <td>False</td>\n      <td>b''</td>\n    </tr>\n  </tbody>\n</table>\n<p>150 rows × 8 columns</p>\n</div>"
     },
     "execution_count": 117,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# open the csv using pandas:\n",
    "import pandas as pd\n",
    "df = pd.read_csv(\"clusts/error/error_results.csv\")\n",
    "# show only rows with success == True:\n",
    "df[df[\"success\"] == False]"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-05-21T12:57:50.962650Z",
     "start_time": "2024-05-21T12:57:50.942197Z"
    }
   },
   "id": "cd93d05c0ca42c7",
   "execution_count": 117
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2024-05-21T12:57:44.631869Z",
     "start_time": "2024-05-21T12:56:35.866071Z"
    }
   },
   "cell_type": "code",
   "execution_count": 115,
   "source": [
    "\n",
    "\n",
    "number_of_chunks = 2868\n",
    "files = glob.glob(\"clusts/opt_lorem_ipsum100k.doc_150*.fasta\")\n",
    "\n",
    "for file in files:\n",
    "    error_correction = get_error_correction_decode(\"reedsolomon\", 2)\n",
    "    dist = get_dist(file)\n",
    "    use_payload_xor = get_payload_xor(file)\n",
    "    seed_spacing = get_seed_spacing(file)\n",
    "    static_number_of_chunks = number_of_chunks\n",
    "    print(f\"Current file and settings: {file}, {dist}, {use_payload_xor}, {seed_spacing}, {static_number_of_chunks}\")\n",
    "    try:\n",
    "        res = decode_from_fasta(file, number_of_chunks=number_of_chunks, dist=dist, error_correction=error_correction,\n",
    "                                use_seed_xor=False, use_payload_xor=use_payload_xor, seed_spacing=seed_spacing,\n",
    "                                use_headerchunk=False)\n",
    "    except Exception as e:\n",
    "        print(f\"Error in {file}: {e}\")\n",
    "        continue"
   ],
   "id": "6f5106e2a128daad",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 0\n",
      "Corrupt Packets : 0\n",
      "<xml><var name=\"_dummy_ret_val\"  />\n",
      "<var name=\"_dummy_ipython_val\"  />\n",
      "<var name=\"_dummy_special_var\"  />\n",
      "<var name=\"RU10Encoder\" type=\"ABCMeta\" qualifier=\"abc\" value=\"%3Cclass %27NOREC4DNA.norec4dna.RU10Encoder.RU10Encoder%27&gt;\" isContainer=\"True\" />\n",
      "<var name=\"__py_debug_temp_var_1001208864\" type=\"int\" qualifier=\"builtins\" value=\"27\" />\n",
      "<var name=\"asdf\" type=\"list\" qualifier=\"builtins\" value=\"%5B%3C used_packets%3A %5B23%2C 300%5D %2C Data%3A %5B104 115  99  51  26  18  29 116  88  60   8  55 153 192 139 231 216 206%0A  20  50   0  52  18%5D &gt;%5D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"ax\" type=\"Axes\" qualifier=\"matplotlib.axes._axes\" value=\"%3CAxes%3A title=%7B%27center%27%3A %27Minimum free energy %28MFE%29 of the generated sequences%27%7D%2C xlabel=%27dna fountain %27&gt;\" isContainer=\"True\" />\n",
      "<var name=\"bmp_low_entropy_diff_dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.            1136.9807546     9091.20111762   12111.88508948%2C   13017.1708098    57959.04100808   71798.24459634   72487.1842063%2C  125647.56019394  167454.99443843  207887.59917079  253583.4801622%2C  261718.31786311  310984.9412345   321695.14945959  368816.37254484%2C  393617.58142113  398484.87252954  446229.27315371  469314.84015955%2C  477620.72923345  482476.68746324  520877.86792584  523718.64231146%2C  567701.29582963  591072.50115539  612037.48997345  628878.87686348%2C  681353.80436257  722346.76126439  770935.25023072  793475.63495812%2C  803332.69084969  847730.75224056  851048.79037268  874467.13097433%2C  903439.69486354  922022.95754105  977234.39739524 1022344.39518796%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
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      "<var name=\"conf_name\" type=\"str\" qualifier=\"builtins\" value=\"sleeping_beauty_dna_fountain_cs23.fasta\" />\n",
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      "<var name=\"counter\" type=\"int\" qualifier=\"builtins\" value=\"0\" />\n",
      "<var name=\"csv_line\" type=\"str\" qualifier=\"builtins\" value=\"file%2Cdist_name%2Cuse_payload_xor%2Cseed_spacing%2Cstatic_number_of_chunks%2Cerror_rate%2Csuccess%2Cdecoded_data%0Aclusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing2_payloadxor.fasta_error_0.05.fasta%2Clow_entropy_evo%2CTrue%2C2%2C2\" />\n",
      "<var name=\"df\" type=\"DataFrame\" qualifier=\"pandas.core.frame\" value=\"%5B%27file%27%2C %27dist_name%27%2C %27use_payload_xor%27%2C %27seed_spacing%27%2C %27static_number_of_chunks%27%2C %27error_rate%27%2C %27success%27%2C %27decoded_data%27%5D %5B0    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   %5D %5B1    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...   evo_compress_encrypt   %5D %5B2    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...  diff_compress_encrypt   %5D %5B3    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   %5D %5B4    clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...        low_entropy_evo   %5D %5B..                                                 ...                    ...   %5D %5B145  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...       low_entropy_diff   %5D %5B146  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...       low_entropy_diff   %5D %5B147  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...                 raptor   %5D %5B148  clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleepi...  diff_compress_encrypt   %5D %5B149  clusts/error/cs_23_I_max_2_hp_10_gc_opt...\" isContainer=\"True\" shape=\"(150, 8)\" />\n",
      "<var name=\"diff_compress_encrypt_high_entropy_dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.               0.           29089.79521874   72481.36996913%2C   98340.54009726  131567.39732824  176222.33645313  228831.95105282%2C  252326.29538902  276175.72445691  299450.09035552  299450.09035552%2C  325747.79207801  350286.21356139  387420.63799373  393380.85543471%2C  438114.97705523  443148.86850801  465291.78684474  507620.53436244%2C  554815.62818098  565762.61188028  587194.87535876  631723.17658683%2C  631723.17658683  651761.53608897  680773.99454248  709201.30476058%2C  744801.68917068  762349.30565287  779814.00716521  785066.34697717%2C  829065.08323761  838672.95527928  858778.80081104  886807.58531494%2C  901742.19919218  922968.09448734  952513.50238877  980596.6076461%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.               0.               0.               0.%2C       0.               0.               0.               0.%2C       0.            5213.34222692   27397.06087366   27397.06087366%2C   27397.06087366   76259.50656745  118731.99703658  118731.99703658%2C  169159.02505416  169159.02505416  169159.02505416  241778.6531302%2C  289301.16954725  289301.16954725  289301.16954725  334042.455604%2C  334042.455604    395036.41601383  428516.1901104   468383.31221304%2C  515536.16651901  552849.46749891  584038.85877362  637743.13880125%2C  677025.87781114  715277.21144298  765344.2744503   822771.30012886%2C  870256.00307536  951876.06719783  995543.61290259 1031900.06437448%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"dist_name\" type=\"str\" qualifier=\"builtins\" value=\"low_entropy_evo\" />\n",
      "<var name=\"encoder\" type=\"RU10Encoder\" qualifier=\"NOREC4DNA.norec4dna.RU10Encoder\" value=\"%3CNOREC4DNA.norec4dna.RU10Encoder.RU10Encoder object at 0x7fea65c13610&gt;\" isContainer=\"True\" />\n",
      "<var name=\"err_list\" type=\"list\" qualifier=\"builtins\" value=\"%5B0%2C 1%2C 2%2C 3%2C 4%2C 5%2C 6%2C 7%5D\" isContainer=\"True\" shape=\"8\" />\n",
      "<var name=\"error_rate\" type=\"float\" qualifier=\"builtins\" value=\"0.05\" />\n",
      "<var name=\"evo_compress_encrypt_high_entropy_dist\" type=\"ndarray\" qualifier=\"numpy\" value=\"%5B      0.            1425.43934062   27002.90907888   43690.73327553%2C   63294.81537234   87788.17204801  121728.30753776  140829.34227724%2C  180834.71376757  208373.25073121  236445.45271099  259943.84686175%2C  290359.40640509  321260.12229916  354279.35337277  382179.33996018%2C  413629.67619777  442249.90271307  469765.28196638  500719.78465128%2C  533697.05550466  561652.23810626  561652.23810626  600011.35261877%2C  624152.76490294  654704.19114975  697183.48788851  724376.2883197%2C  751004.84422912  771229.47574536  797325.55293154  823503.60307259%2C  854062.55679468  890863.07690872  910159.55153303  938570.27144896%2C  963145.65800847  979819.7521839  1013685.83134719 1043822.30710253%2C 1048576.        %5D\" isContainer=\"True\" shape=\"(41,)\" />\n",
      "<var name=\"fig\" type=\"Figure\" qualifier=\"matplotlib.figure\" value=\"%3CFigure size 640x480 with 1 Axes&gt;\" isContainer=\"True\" />\n",
      "<var name=\"file\" type=\"str\" qualifier=\"builtins\" value=\"clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing4.fasta_error_0.05.fasta\" />\n",
      "<var name=\"files\" type=\"list\" qualifier=\"builtins\" value=\"%5B%27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing2_payloadxor.fasta_error_0.05.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_evo_compress_encrypt_high_entropy_dist_seedspacing2.fasta_error_0.01.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_diff_compress_encrypt_high_entropy_dist_seedspacing2.fasta_error_0.05.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing4_payloadxor.fasta_error_0.01.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_bmp_low_entropy_evo_dist_seedspacing2.fasta_error_0.01.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_evo_compress_encrypt_high_entropy_dist_seedspacing2_payloadxor.fasta_error_0.03.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing4.fasta_error_0.03.fasta%27%2C %27clusts/error/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_diff_compres...\" isContainer=\"True\" shape=\"150\" />\n",
      "<var name=\"grass_enc\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%270%27%3A %27CGCCCGATACTCCACGAGACAACAACACATACAATAGACGCAGAGACGATACCGAATCTGGGTGCGGTCGTGGTGGTCGCGGACCTATGCACGCGTGACCATAATTCGCCGGAGCGA%27%2C %271%27%3A %27CGACTACCGCATATGAAGCCAACAACAGGTACTAACCACAGACGTCGTTAGGAGCCGCCATGAACTCGTGTGGATGTACAGTCACTCCAGAATGGCAACCTCCCGAGCATGTAGCCG%27%2C %2710%27%3A %27TTATCTGAGGAGCCTATAGTAACAACAATCCACCACAGTCTGCGTAGCCTATAGGTACTGGGTGGACCAAGCAGTCGTGATGCGCCACCATATGACTTAACTATAGAGCGACATGTA%27%2C %27100%27%3A %27GGCTACCCTGACATACGCGGAGCAACAGTAGGTCGTTGAAATTTGCCACTAGCAAACACGTAGGCTCTGCATCCAGTCCTCCGCTCGTGAATCCCAGCTCTCCTGTACGCTCGTCAT%27%2C %27101%27%3A %27CTCTGAACACGACCTCGTTGAGCAACAGGAACGATCTCTGGTCACCTCAGTTTAGTCCCAGGCTACGTACGTTCTGGACAGTTGCACAAGACTTGACCGGTCGTCTAGTCAGAGGGA%27%2C %27102%27%3A %27GGCAAGACGGAGGAGGAGATAGCAACATCTGGATATGTCGCATTGAATCACGTCGCAAACGAGGAGGTACCACCTAGTGTAGCTGCAGGTCCAGCATATCCATTGACACTCCAGCAT%27%2C %27103%27%3A %27TTAAACCGTAACATGTGACTAGCAACACACAGAAAGACTCCACTCTTATTGGGTGTACTGAATCCTCGTGCTCATTAGCTGTCGTTGCTCTGAGTGCCGATCATCCCATTGGACCGC%27%2C %27104%27%3A %27GTCCGTGAGGACAGTTATGTAGCAACACGATCGTTAGTCCCTTCGAGAGCATGCGATTCGCCAAATACAGGCCCGCGATTACTGGGAGCTCCGGATGCTA...\" isContainer=\"True\" shape=\"713\" />\n",
      "<var name=\"in_file\" type=\"str\" qualifier=\"builtins\" value=\"cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta\" />\n",
      "<var name=\"in_folder\" type=\"str\" qualifier=\"builtins\" value=\"clusts/\" />\n",
      "<var name=\"in_path\" type=\"str\" qualifier=\"builtins\" value=\"clusts/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta\" />\n",
      "<var name=\"intermediate_symbols\" type=\"_lru_cache_wrapper\" qualifier=\"functools\" value=\"%3Cfunctools._lru_cache_wrapper object at 0x7fea85a7e610&gt;\" isContainer=\"True\" />\n",
      "<var name=\"iterations\" type=\"int\" qualifier=\"builtins\" value=\"1\" />\n",
      "<var name=\"key\" type=\"str\" qualifier=\"builtins\" value=\"packet\" />\n",
      "<var name=\"key_title\" type=\"str\" qualifier=\"builtins\" value=\"dna fountain \" />\n",
      "<var name=\"length\" type=\"str\" qualifier=\"builtins\" value=\"CGCCCGATACTCCACGAGACAACAACACATACAATAGACGCAGAGACGATACCGAATCTGGGTGCGGTCGTGGTGGTCGCGGACCTATGCACGCGTGACCATAATTCGCCGGAGCGACGACTACCGCATATGAAGCCAACAACAGGTACTAACCACAGACGTCGTTAGGAGCCGCCATGAACTCGTGTGGATGTACAGTCACTCCAGAATGGCAACCTCCCGAGCATGTAGCCGACGCGCCGAAACCAGAAGGCAA\" />\n",
      "<var name=\"number_of_chunks\" type=\"int\" qualifier=\"builtins\" value=\"289\" />\n",
      "<var name=\"o_\" type=\"TextIOWrapper\" qualifier=\"_io\" value=\"%3C_io.TextIOWrapper name=%27clusts/error/error_results.csv%27 mode=%27w%27 encoding=%27UTF-8%27&gt;\" isContainer=\"True\" />\n",
      "<var name=\"out\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%27packet%27%3A %5B%27clusts/sleeping_Teauty_dna_fountain_cs23.fasta%27%5D%7D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"out_path\" type=\"str\" qualifier=\"builtins\" value=\"clusts/error_test/cs_23_I_max_2_hp_10_gc_opt_sleeping_beauty_150_raptor_seedspacing0_payloadxor.fasta\" />\n",
      "<var name=\"probs\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%27deletion%27%3A 10%2C %27insertion%27%3A 10%2C %27substitution%27%3A 80%7D\" isContainer=\"True\" shape=\"3\" />\n",
      "<var name=\"raptor_dist\" type=\"list\" qualifier=\"builtins\" value=\"%5B0%2C 10241%2C 491582%2C 712794%2C 831695%2C 831695%2C 831695%2C 831695%2C 831695%2C 831695%2C 948446%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1032189%2C 1048576%5D\" isContainer=\"True\" shape=\"41\" />\n",
      "<var name=\"res\" type=\"tuple\" qualifier=\"builtins\" value=\"%28False%2C %27%27%29\" isContainer=\"True\" shape=\"2\" />\n",
      "<var name=\"results\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%270%27%3A %7B%7D%2C %27params%27%3A %7B%27err_type%27%3A %7B%27deletion%27%3A 10%2C %27insertion%27%3A 10%2C %27substitution%27%3A 80%7D%2C %27errs_weights%27%3A %5B0.15%2C 0.15%2C 0.25%2C 0.2%2C 0.1%2C 0.06%2C 0.05%2C 0.04%5D%2C %27num_errs%27%3A %5B0%2C 1%2C 2%2C 3%2C 4%2C 5%2C 6%2C 7%5D%7D%7D\" isContainer=\"True\" shape=\"2\" />\n",
      "<var name=\"seed_spacing\" type=\"int\" qualifier=\"builtins\" value=\"4\" />\n",
      "<var name=\"seqs\" type=\"dict\" qualifier=\"builtins\" value=\"%7B%27packet%27%3A %27CCACCCGTGACTGTGTAGCTACTACGTCCCACAATAAAGAAATCCGTAACAGCCAGAAGCCCAGCACTACATCCCTCAGTCACGAAATCATGGCCTTTCCGTTACATTATTAGGAC%27%7D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"start\" type=\"float\" qualifier=\"builtins\" value=\"1716292093.6295974\" />\n",
      "<var name=\"static_number_of_chunks\" type=\"int\" qualifier=\"builtins\" value=\"289\" />\n",
      "<var name=\"time\" type=\"builtin_function_or_method\" qualifier=\"builtins\" value=\"%3Cbuilt-in function time&gt;\" isContainer=\"True\" />\n",
      "<var name=\"total_nts\" type=\"int\" qualifier=\"builtins\" value=\"116\" />\n",
      "<var name=\"use_payload_xor\" type=\"bool\" qualifier=\"builtins\" value=\"False\" />\n",
      "<var name=\"value\" type=\"list\" qualifier=\"builtins\" value=\"%5B%27clusts/sleeping_Teauty_dna_fountain_cs23.fasta%27%5D\" isContainer=\"True\" shape=\"1\" />\n",
      "<var name=\"weights\" type=\"list\" qualifier=\"builtins\" value=\"%5B0.15%2C 0.15%2C 0.25%2C 0.2%2C 0.1%2C 0.06%2C 0.05%2C 0.04%5D\" isContainer=\"True\" shape=\"8\" />\n",
      "</xml>\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing6_payloadxor.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), True, 6, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 653\n",
      "Corrupt Packets : 4091\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing6_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing2_payloadxor.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), True, 2, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 719\n",
      "Corrupt Packets : 3881\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing2_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing5.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), False, 5, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 738\n",
      "Corrupt Packets : 3917\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing5.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing0_payloadxor.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), True, 0, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 4710\n",
      "Corrupt Packets : 0\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing0_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing3_payloadxor.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), True, 3, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 690\n",
      "Corrupt Packets : 3953\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing3_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing3.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), False, 3, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 674\n",
      "Corrupt Packets : 3989\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing3.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing1_payloadxor.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), True, 1, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 700\n",
      "Corrupt Packets : 3953\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing1_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing8.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), False, 8, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 634\n",
      "Corrupt Packets : 3760\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing8.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing4_payloadxor.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), True, 4, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 715\n",
      "Corrupt Packets : 3902\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing4_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing7.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), False, 7, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 667\n",
      "Corrupt Packets : 3733\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing7.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing2.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), False, 2, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 692\n",
      "Corrupt Packets : 3976\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing2.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing2_payloadxor.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), True, 2, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 704\n",
      "Corrupt Packets : 4035\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing2_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing0.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), False, 0, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 4685\n",
      "Corrupt Packets : 0\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing0.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing7_payloadxor.fasta, (array([      0.        ,       0.        ,   29089.79521874,\n",
      "         72481.36996913,   98340.54009726,  131567.39732824,\n",
      "        176222.33645313,  228831.95105282,  252326.29538902,\n",
      "        276175.72445691,  299450.09035552,  299450.09035552,\n",
      "        325747.79207801,  350286.21356139,  387420.63799373,\n",
      "        393380.85543471,  438114.97705523,  443148.86850801,\n",
      "        465291.78684474,  507620.53436244,  554815.62818098,\n",
      "        565762.61188028,  587194.87535876,  631723.17658683,\n",
      "        631723.17658683,  651761.53608897,  680773.99454248,\n",
      "        709201.30476058,  744801.68917068,  762349.30565287,\n",
      "        779814.00716521,  785066.34697717,  829065.08323761,\n",
      "        838672.95527928,  858778.80081104,  886807.58531494,\n",
      "        901742.19919218,  922968.09448734,  952513.50238877,\n",
      "        980596.6076461 , 1048576.        ]), 'diff_compress_encrypt'), True, 7, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 736\n",
      "Corrupt Packets : 3972\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing7_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing7.fasta, (array([      0.        ,       0.        ,   29089.79521874,\n",
      "         72481.36996913,   98340.54009726,  131567.39732824,\n",
      "        176222.33645313,  228831.95105282,  252326.29538902,\n",
      "        276175.72445691,  299450.09035552,  299450.09035552,\n",
      "        325747.79207801,  350286.21356139,  387420.63799373,\n",
      "        393380.85543471,  438114.97705523,  443148.86850801,\n",
      "        465291.78684474,  507620.53436244,  554815.62818098,\n",
      "        565762.61188028,  587194.87535876,  631723.17658683,\n",
      "        631723.17658683,  651761.53608897,  680773.99454248,\n",
      "        709201.30476058,  744801.68917068,  762349.30565287,\n",
      "        779814.00716521,  785066.34697717,  829065.08323761,\n",
      "        838672.95527928,  858778.80081104,  886807.58531494,\n",
      "        901742.19919218,  922968.09448734,  952513.50238877,\n",
      "        980596.6076461 , 1048576.        ]), 'diff_compress_encrypt'), False, 7, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 707\n",
      "Corrupt Packets : 3905\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing7.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing8.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), False, 8, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 695\n",
      "Corrupt Packets : 3980\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing8.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing7_payloadxor.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), True, 7, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 658\n",
      "Corrupt Packets : 3965\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing7_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing8.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), False, 8, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 690\n",
      "Corrupt Packets : 3919\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing8.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing2_payloadxor.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), True, 2, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 685\n",
      "Corrupt Packets : 4025\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing2_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing0_payloadxor.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), True, 0, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 4657\n",
      "Corrupt Packets : 0\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing0_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing3.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), False, 3, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 684\n",
      "Corrupt Packets : 3725\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing3.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing1_payloadxor.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), True, 1, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 734\n",
      "Corrupt Packets : 3883\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing1_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing4.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), False, 4, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 668\n",
      "Corrupt Packets : 3929\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing4.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing3_payloadxor.fasta, (array([      0.        ,       0.        ,   29089.79521874,\n",
      "         72481.36996913,   98340.54009726,  131567.39732824,\n",
      "        176222.33645313,  228831.95105282,  252326.29538902,\n",
      "        276175.72445691,  299450.09035552,  299450.09035552,\n",
      "        325747.79207801,  350286.21356139,  387420.63799373,\n",
      "        393380.85543471,  438114.97705523,  443148.86850801,\n",
      "        465291.78684474,  507620.53436244,  554815.62818098,\n",
      "        565762.61188028,  587194.87535876,  631723.17658683,\n",
      "        631723.17658683,  651761.53608897,  680773.99454248,\n",
      "        709201.30476058,  744801.68917068,  762349.30565287,\n",
      "        779814.00716521,  785066.34697717,  829065.08323761,\n",
      "        838672.95527928,  858778.80081104,  886807.58531494,\n",
      "        901742.19919218,  922968.09448734,  952513.50238877,\n",
      "        980596.6076461 , 1048576.        ]), 'diff_compress_encrypt'), True, 3, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 726\n",
      "Corrupt Packets : 3931\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing3_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing6_payloadxor.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), True, 6, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 717\n",
      "Corrupt Packets : 3899\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing6_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing5_payloadxor.fasta, (array([      0.        ,       0.        ,   29089.79521874,\n",
      "         72481.36996913,   98340.54009726,  131567.39732824,\n",
      "        176222.33645313,  228831.95105282,  252326.29538902,\n",
      "        276175.72445691,  299450.09035552,  299450.09035552,\n",
      "        325747.79207801,  350286.21356139,  387420.63799373,\n",
      "        393380.85543471,  438114.97705523,  443148.86850801,\n",
      "        465291.78684474,  507620.53436244,  554815.62818098,\n",
      "        565762.61188028,  587194.87535876,  631723.17658683,\n",
      "        631723.17658683,  651761.53608897,  680773.99454248,\n",
      "        709201.30476058,  744801.68917068,  762349.30565287,\n",
      "        779814.00716521,  785066.34697717,  829065.08323761,\n",
      "        838672.95527928,  858778.80081104,  886807.58531494,\n",
      "        901742.19919218,  922968.09448734,  952513.50238877,\n",
      "        980596.6076461 , 1048576.        ]), 'diff_compress_encrypt'), True, 5, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 724\n",
      "Corrupt Packets : 3944\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing5_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing6.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), False, 6, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 650\n",
      "Corrupt Packets : 3793\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing6.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing1.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), False, 1, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 705\n",
      "Corrupt Packets : 3661\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing1.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing0.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), False, 0, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 4355\n",
      "Corrupt Packets : 0\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing0.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing5_payloadxor.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), True, 5, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 690\n",
      "Corrupt Packets : 3908\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing5_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing4.fasta, ([0, 10241, 491582, 712794, 831695, 831695, 831695, 831695, 831695, 831695, 948446, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1032189, 1048576], 'raptor'), False, 4, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 637\n",
      "Corrupt Packets : 3786\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_raptor_seedspacing4.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing1.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), False, 1, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 677\n",
      "Corrupt Packets : 3996\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing1.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing6.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), False, 6, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 669\n",
      "Corrupt Packets : 4035\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing6.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing3.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), False, 3, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 671\n",
      "Corrupt Packets : 3906\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing3.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing8_payloadxor.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), True, 8, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 702\n",
      "Corrupt Packets : 3931\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing8_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing3_payloadxor.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), True, 3, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 685\n",
      "Corrupt Packets : 3918\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing3_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing2.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), False, 2, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 704\n",
      "Corrupt Packets : 3888\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing2.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing0_payloadxor.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), True, 0, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 4583\n",
      "Corrupt Packets : 0\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing0_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing7.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), False, 7, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 684\n",
      "Corrupt Packets : 4006\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing7.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing3.fasta, (array([      0.        ,       0.        ,   29089.79521874,\n",
      "         72481.36996913,   98340.54009726,  131567.39732824,\n",
      "        176222.33645313,  228831.95105282,  252326.29538902,\n",
      "        276175.72445691,  299450.09035552,  299450.09035552,\n",
      "        325747.79207801,  350286.21356139,  387420.63799373,\n",
      "        393380.85543471,  438114.97705523,  443148.86850801,\n",
      "        465291.78684474,  507620.53436244,  554815.62818098,\n",
      "        565762.61188028,  587194.87535876,  631723.17658683,\n",
      "        631723.17658683,  651761.53608897,  680773.99454248,\n",
      "        709201.30476058,  744801.68917068,  762349.30565287,\n",
      "        779814.00716521,  785066.34697717,  829065.08323761,\n",
      "        838672.95527928,  858778.80081104,  886807.58531494,\n",
      "        901742.19919218,  922968.09448734,  952513.50238877,\n",
      "        980596.6076461 , 1048576.        ]), 'diff_compress_encrypt'), False, 3, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 748\n",
      "Corrupt Packets : 3912\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing3.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing5_payloadxor.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), True, 5, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 763\n",
      "Corrupt Packets : 4007\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing5_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing4.fasta, (array([      0.        ,    1425.43934062,   27002.90907888,\n",
      "         43690.73327553,   63294.81537234,   87788.17204801,\n",
      "        121728.30753776,  140829.34227724,  180834.71376757,\n",
      "        208373.25073121,  236445.45271099,  259943.84686175,\n",
      "        290359.40640509,  321260.12229916,  354279.35337277,\n",
      "        382179.33996018,  413629.67619777,  442249.90271307,\n",
      "        469765.28196638,  500719.78465128,  533697.05550466,\n",
      "        561652.23810626,  561652.23810626,  600011.35261877,\n",
      "        624152.76490294,  654704.19114975,  697183.48788851,\n",
      "        724376.2883197 ,  751004.84422912,  771229.47574536,\n",
      "        797325.55293154,  823503.60307259,  854062.55679468,\n",
      "        890863.07690872,  910159.55153303,  938570.27144896,\n",
      "        963145.65800847,  979819.7521839 , 1013685.83134719,\n",
      "       1043822.30710253, 1048576.        ]), 'evo_compress_encrypt'), False, 4, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 705\n",
      "Corrupt Packets : 3988\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_evo_compress_encrypt_high_entropy_dist_seedspacing4.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing5_payloadxor.fasta, (array([      0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "             0.        ,       0.        ,       0.        ,\n",
      "          5213.34222692,   27397.06087366,   27397.06087366,\n",
      "         27397.06087366,   76259.50656745,  118731.99703658,\n",
      "        118731.99703658,  169159.02505416,  169159.02505416,\n",
      "        169159.02505416,  241778.6531302 ,  289301.16954725,\n",
      "        289301.16954725,  289301.16954725,  334042.455604  ,\n",
      "        334042.455604  ,  395036.41601383,  428516.1901104 ,\n",
      "        468383.31221304,  515536.16651901,  552849.46749891,\n",
      "        584038.85877362,  637743.13880125,  677025.87781114,\n",
      "        715277.21144298,  765344.2744503 ,  822771.30012886,\n",
      "        870256.00307536,  951876.06719783,  995543.61290259,\n",
      "       1031900.06437448, 1048576.        ]), 'low_entropy_evo'), True, 5, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 692\n",
      "Corrupt Packets : 3933\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_evo_dist_seedspacing5_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing7_payloadxor.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), True, 7, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 714\n",
      "Corrupt Packets : 3906\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing7_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing8_payloadxor.fasta, (array([      0.        ,       0.        ,   29089.79521874,\n",
      "         72481.36996913,   98340.54009726,  131567.39732824,\n",
      "        176222.33645313,  228831.95105282,  252326.29538902,\n",
      "        276175.72445691,  299450.09035552,  299450.09035552,\n",
      "        325747.79207801,  350286.21356139,  387420.63799373,\n",
      "        393380.85543471,  438114.97705523,  443148.86850801,\n",
      "        465291.78684474,  507620.53436244,  554815.62818098,\n",
      "        565762.61188028,  587194.87535876,  631723.17658683,\n",
      "        631723.17658683,  651761.53608897,  680773.99454248,\n",
      "        709201.30476058,  744801.68917068,  762349.30565287,\n",
      "        779814.00716521,  785066.34697717,  829065.08323761,\n",
      "        838672.95527928,  858778.80081104,  886807.58531494,\n",
      "        901742.19919218,  922968.09448734,  952513.50238877,\n",
      "        980596.6076461 , 1048576.        ]), 'diff_compress_encrypt'), True, 8, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 685\n",
      "Corrupt Packets : 3988\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing8_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing2_payloadxor.fasta, (array([      0.        ,       0.        ,   29089.79521874,\n",
      "         72481.36996913,   98340.54009726,  131567.39732824,\n",
      "        176222.33645313,  228831.95105282,  252326.29538902,\n",
      "        276175.72445691,  299450.09035552,  299450.09035552,\n",
      "        325747.79207801,  350286.21356139,  387420.63799373,\n",
      "        393380.85543471,  438114.97705523,  443148.86850801,\n",
      "        465291.78684474,  507620.53436244,  554815.62818098,\n",
      "        565762.61188028,  587194.87535876,  631723.17658683,\n",
      "        631723.17658683,  651761.53608897,  680773.99454248,\n",
      "        709201.30476058,  744801.68917068,  762349.30565287,\n",
      "        779814.00716521,  785066.34697717,  829065.08323761,\n",
      "        838672.95527928,  858778.80081104,  886807.58531494,\n",
      "        901742.19919218,  922968.09448734,  952513.50238877,\n",
      "        980596.6076461 , 1048576.        ]), 'diff_compress_encrypt'), True, 2, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 701\n",
      "Corrupt Packets : 3970\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_diff_compress_encrypt_high_entropy_dist_seedspacing2_payloadxor.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing4.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), False, 4, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Decoded Packets: 709\n",
      "Corrupt Packets : 3997\n",
      "Error in clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing4.fasta: 'NoneType' object has no attribute 'isPotentionallySolvable'\n",
      "Current file and settings: clusts/opt_lorem_ipsum100k.doc_150_bmp_low_entropy_diff_dist_seedspacing2_payloadxor.fasta, (array([      0.        ,    1136.9807546 ,    9091.20111762,\n",
      "         12111.88508948,   13017.1708098 ,   57959.04100808,\n",
      "         71798.24459634,   72487.1842063 ,  125647.56019394,\n",
      "        167454.99443843,  207887.59917079,  253583.4801622 ,\n",
      "        261718.31786311,  310984.9412345 ,  321695.14945959,\n",
      "        368816.37254484,  393617.58142113,  398484.87252954,\n",
      "        446229.27315371,  469314.84015955,  477620.72923345,\n",
      "        482476.68746324,  520877.86792584,  523718.64231146,\n",
      "        567701.29582963,  591072.50115539,  612037.48997345,\n",
      "        628878.87686348,  681353.80436257,  722346.76126439,\n",
      "        770935.25023072,  793475.63495812,  803332.69084969,\n",
      "        847730.75224056,  851048.79037268,  874467.13097433,\n",
      "        903439.69486354,  922022.95754105,  977234.39739524,\n",
      "       1022344.39518796, 1048576.        ]), 'low_entropy_diff'), True, 2, 2868\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|       | Correct: 0, Corrupt: ------, ETA:  --:--:-- Elapsed Time: 0:00:00"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
      "\u001B[0;31mKeyboardInterrupt\u001B[0m                         Traceback (most recent call last)",
      "Cell \u001B[0;32mIn[115], line 12\u001B[0m\n\u001B[1;32m     10\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mCurrent file and settings: \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mfile\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m, \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mdist\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m, \u001B[39m\u001B[38;5;132;01m{\u001B[39;00muse_payload_xor\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m, \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mseed_spacing\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m, \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mstatic_number_of_chunks\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m     11\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m---> 12\u001B[0m     res \u001B[38;5;241m=\u001B[39m \u001B[43mdecode_from_fasta\u001B[49m\u001B[43m(\u001B[49m\u001B[43mfile\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mnumber_of_chunks\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mnumber_of_chunks\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mdist\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mdist\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43merror_correction\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43merror_correction\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m     13\u001B[0m \u001B[43m                            \u001B[49m\u001B[43muse_seed_xor\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43muse_payload_xor\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43muse_payload_xor\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mseed_spacing\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mseed_spacing\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m     14\u001B[0m \u001B[43m                            \u001B[49m\u001B[43muse_headerchunk\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43;01mFalse\u001B[39;49;00m\u001B[43m)\u001B[49m\n\u001B[1;32m     15\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m     16\u001B[0m     \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mError in \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mfile\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m: \u001B[39m\u001B[38;5;132;01m{\u001B[39;00me\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m\"\u001B[39m)\n",
      "Cell \u001B[0;32mIn[97], line 32\u001B[0m, in \u001B[0;36mdecode_from_fasta\u001B[0;34m(filename, number_of_chunks, dist, error_correction, use_seed_xor, use_payload_xor, seed_spacing, use_headerchunk)\u001B[0m\n\u001B[1;32m     30\u001B[0m decoder\u001B[38;5;241m.\u001B[39mcreateAuxBlocks()\n\u001B[1;32m     31\u001B[0m decoder\u001B[38;5;241m.\u001B[39mprogress_bar \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39mcreate_progress_bar(number_of_chunks \u001B[38;5;241m+\u001B[39m \u001B[38;5;241m0.02\u001B[39m \u001B[38;5;241m*\u001B[39m number_of_chunks)\n\u001B[0;32m---> 32\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[43mdecoder\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdecodeFile\u001B[49m\u001B[43m(\u001B[49m\u001B[43mid_len_format\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mI\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[1;32m     33\u001B[0m \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mSuccess: \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mres\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m     34\u001B[0m res_data \u001B[38;5;241m=\u001B[39m decoder\u001B[38;5;241m.\u001B[39msaveDecodedFile(last_chunk_len_format\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124m\"\u001B[39m, null_is_terminator\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mFalse\u001B[39;00m, print_to_output\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mFalse\u001B[39;00m,\n\u001B[1;32m     35\u001B[0m                         partial_decoding\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mTrue\u001B[39;00m)\n",
      "File \u001B[0;32m~/Code/OFC4DNA/NOREC4DNA/norec4dna/RU10Decoder.py:244\u001B[0m, in \u001B[0;36mRU10Decoder.decodeFile\u001B[0;34m(self, packet_len_format, crc_len_format, number_of_chunks_len_format, id_len_format)\u001B[0m\n\u001B[1;32m    242\u001B[0m raw_packet_list\u001B[38;5;241m.\u001B[39mappend((error_prob, seed, dna_str))\n\u001B[1;32m    243\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 244\u001B[0m     new_pack \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mparse_raw_packet(BytesIO(\u001B[43mtranlate_quat_to_byte\u001B[49m\u001B[43m(\u001B[49m\u001B[43mdna_str\u001B[49m\u001B[43m)\u001B[49m)\u001B[38;5;241m.\u001B[39mread(),\n\u001B[1;32m    245\u001B[0m                                      crc_len_format\u001B[38;5;241m=\u001B[39mcrc_len_format,\n\u001B[1;32m    246\u001B[0m                                      number_of_chunks_len_format\u001B[38;5;241m=\u001B[39mnumber_of_chunks_len_format,\n\u001B[1;32m    247\u001B[0m                                      packet_len_format\u001B[38;5;241m=\u001B[39mpacket_len_format,\n\u001B[1;32m    248\u001B[0m                                      id_len_format\u001B[38;5;241m=\u001B[39mid_len_format)\n\u001B[1;32m    249\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m:\n\u001B[1;32m    250\u001B[0m     new_pack \u001B[38;5;241m=\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mCORRUPT\u001B[39m\u001B[38;5;124m\"\u001B[39m\n",
      "File \u001B[0;32m~/Code/OFC4DNA/venv/lib/python3.10/site-packages/norec4dna/helper/quaternary2Bin.py:50\u001B[0m, in \u001B[0;36mtranlate_quat_to_byte\u001B[0;34m(in_txt)\u001B[0m\n\u001B[1;32m     48\u001B[0m out \u001B[38;5;241m=\u001B[39m \u001B[38;5;124mb\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m'\u001B[39m\n\u001B[1;32m     49\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m i \u001B[38;5;129;01min\u001B[39;00m \u001B[38;5;28mrange\u001B[39m(\u001B[38;5;241m0\u001B[39m, \u001B[38;5;28mlen\u001B[39m(in_txt), \u001B[38;5;241m4\u001B[39m):\n\u001B[0;32m---> 50\u001B[0m     out \u001B[38;5;241m+\u001B[39m\u001B[38;5;241m=\u001B[39m \u001B[43mquats_to_bytes\u001B[49m\u001B[43m(\u001B[49m\u001B[43min_txt\u001B[49m\u001B[43m[\u001B[49m\u001B[43mi\u001B[49m\u001B[43m:\u001B[49m\u001B[43mi\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m+\u001B[39;49m\u001B[43m \u001B[49m\u001B[38;5;241;43m4\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m     51\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m out\n",
      "File \u001B[0;32m~/Code/OFC4DNA/venv/lib/python3.10/site-packages/norec4dna/helper/quaternary2Bin.py:43\u001B[0m, in \u001B[0;36mquats_to_bytes\u001B[0;34m(quats)\u001B[0m\n\u001B[1;32m     41\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mquats_to_bytes\u001B[39m(quats: typing\u001B[38;5;241m.\u001B[39mAnyStr) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m \u001B[38;5;28mbytes\u001B[39m:\n\u001B[1;32m     42\u001B[0m     \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43m(\u001B[49m\u001B[43m(\u001B[49m\u001B[43mget_quarter_byte\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquats\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m0\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m<<\u001B[39;49m\u001B[43m \u001B[49m\u001B[38;5;241;43m6\u001B[39;49m\u001B[43m)\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m+\u001B[39;49m\u001B[43m \u001B[49m\u001B[43m(\u001B[49m\u001B[43mget_quarter_byte\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquats\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m1\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m<<\u001B[39;49m\u001B[43m \u001B[49m\u001B[38;5;241;43m4\u001B[39;49m\u001B[43m)\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m+\u001B[39;49m\u001B[43m \u001B[49m\u001B[43m(\u001B[49m\u001B[43mget_quarter_byte\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquats\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m2\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m<<\u001B[39;49m\u001B[43m \u001B[49m\u001B[38;5;241;43m2\u001B[39;49m\u001B[43m)\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m+\u001B[39;49m\u001B[43m \u001B[49m\u001B[43m(\u001B[49m\n\u001B[0;32m---> 43\u001B[0m \u001B[43m        \u001B[49m\u001B[43mget_quarter_byte\u001B[49m\u001B[43m(\u001B[49m\u001B[43mquats\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m3\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\u001B[43m)\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mto_bytes\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;241;43m1\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[38;5;124;43mbig\u001B[39;49m\u001B[38;5;124;43m\"\u001B[39;49m\u001B[43m)\u001B[49m\n",
      "\u001B[0;31mKeyboardInterrupt\u001B[0m: "
     ]
    }
   ]
  }
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