cleans up trim_seq and bloom_example

knightlab-analyses · Nov 11, 2016 · 698a4e1 · 698a4e1
1 parent 555aa5e
commit 698a4e1
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 34 deletions.
diff --git a/bloom/filter_seqs_from_biom.py b/bloom/filter_seqs_from_biom.py
@@ -44,7 +44,7 @@ def remove_seqs(table, seqs):
     biom.Table
     """
     filter_seqs = {str(s) for s in seqs}
-    _filter = lambda v, i, m: i in filter_seqs
+    _filter = lambda v, i, m: i not in filter_seqs
     return table.filter(_filter, axis='observation', inplace=False)
 
 

diff --git a/ipynb/bloom_example.ipynb b/ipynb/bloom_example.ipynb
@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "collapsed": false
    },
@@ -36,15 +36,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {
     "collapsed": false
    },
    "outputs": [],
    "source": [
     "data_dir = '../data/'\n",
     "results_dir = '../results'\n",
-    "seqs_file = '30_seqs.fna'\n",
+    "seqs_file = '../data/newbloom.all.fna'\n",
     "biom_file = 'erc.qiita-1481.biom'\n",
     "filtered_file = 'filtered.fna'\n",
     "\n",
@@ -53,32 +53,6 @@
     "filtered_file = os.path.join(results_dir, filtered_file)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "And we'll unzip the zip file to extract the sequences."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "gunzip: can't stat: ../data/30_seqs.fna.gz (../data/30_seqs.fna.gz.gz): No such file or directory\r\n"
-     ]
-    }
-   ],
-   "source": [
-    "!gunzip ../data/30_seqs.fna.gz"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -91,7 +65,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {
     "collapsed": false
    },
@@ -111,7 +85,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false
    },
@@ -130,7 +104,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 9,
    "metadata": {
     "collapsed": true
    },
@@ -141,7 +115,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {
     "collapsed": false
    },