From 19df3c36b5b1b4328b5722123c4fc0daa1eff3ea Mon Sep 17 00:00:00 2001 From: Giuseppe Profiti Date: Fri, 18 Mar 2016 17:18:49 +0100 Subject: [PATCH] First commit of last year code --- LICENSE.txt | 339 ++++++++++++++++++++++++++++++++++++++ Makefile | 2 + README.txt | 81 ++++++++++ alignbucket.sh | 18 +++ bucketize.py | 31 ++++ src/alignbucket.cpp | 386 ++++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 857 insertions(+) create mode 100644 LICENSE.txt create mode 100644 Makefile create mode 100644 README.txt create mode 100644 alignbucket.sh create mode 100644 bucketize.py create mode 100644 src/alignbucket.cpp diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..d159169 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,339 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..2fdd7e2 --- /dev/null +++ b/Makefile @@ -0,0 +1,2 @@ +alignbucket: + g++ -o alignbucket src/alignbucket.cpp -lgmpxx -lgmp -lboost_program_options diff --git a/README.txt b/README.txt new file mode 100644 index 0000000..1524c48 --- /dev/null +++ b/README.txt @@ -0,0 +1,81 @@ +Documentation +------------------ + +AlignBucket is a software for splitting a fasta file into smaller pieces suitable for +alignment with BLAST. The constraint used to optimize the result is the required +minimum alignment coverage. + + +Requirements +------------------ +The program was tested on a GNU/Linux Debian 7 system. + +The required libraries are: +- GNU Multiple Precision library (gmp) +- boost (at least version 1.49) + +Also Python version >= 2.6.6 is required for some helper functions. + +Archive content +------------------ +The archive alignbucket.zip contains: + - src/alignbucket.cpp (source code) + - bucketize.py (helper functions) + - alignbucket.sh (main executable script) + - Makefile + - LICENSE.txt + - README.txt (this file) + + +Compilation +------------------ + +To compile the program, you need to install the required libraries. +On Debian and Ubuntu you can use the following commands: + + sudo apt-get install g++ + sudo apt-get install libgmp3-dev + sudo apt-get install libboost-dev + sudo apt-get install libboost-program-options-dev + +Then you must run: + + make + +or, if you don't have Automake in your system: + g++ -o alignbucket src/alignbucket.cpp -lgmpxx -lgmp -lboost_program_options + +Then, you have to set execution permission on the program: + chmod u+x alignbucket + + +Usage +------------------ +To split your fasta file into optimized buckets for 90% coverage, just run the +following command: + ./alignbucket.sh + +Example with Swissprot sequences: + ./alignbucket.sh uniprot_sprot.fasta + +The output will be a set of fasta file named xxx-yyy.fasta, with xxx and yyy +being the minimum and the maximum length of the sequences inside the file. + + +For different coverage ratios, just run + ./alignbucket.sh + +Example, for 75% coverage use: + ./alignbucket.sh uniprot_sprot.fasta 75 + + +Authors +---------------- + +Giuseppe Profiti +Piero Fariselli + +License +---------------- +The program is released under a GNU Public License version 2. Please see the +LICENSE.txt file diff --git a/alignbucket.sh b/alignbucket.sh new file mode 100644 index 0000000..3312cea --- /dev/null +++ b/alignbucket.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +F=$1 + +function process { + echo "Buckets identified, writing fasta files..." + python bucketize.py $F && rm buckets.list +} + +if [ "$#" -lt 1 ]; then + echo "Usage: ./alignbucket.sh []" +elif [ "$#" -eq 1 ]; then + ./alignbucket -f $F && process +elif [ "$#" -eq 2 ]; then + ./alignbucket -f $F --delta $2 && process +else + echo "Usage: ./alignbucket.sh []" +fi diff --git a/bucketize.py b/bucketize.py new file mode 100644 index 0000000..d0bf4e6 --- /dev/null +++ b/bucketize.py @@ -0,0 +1,31 @@ +import sys + +source = sys.argv[1] + +d = dict() + +f = open("buckets.list") +for r in f: + r = r.rstrip() + seq,b = r.split("\t") + if seq in d: + d[seq].append(b) + else: + d[seq] = [b] + +f.close() + +f = open(source) +buckets = [] +for r in f: + seq = r.rstrip() + if seq[0]==">": + for b in buckets: + b.close() + buckets = list(map(lambda x: open(x+".fasta","a"), d.get(seq[1:],[]))) + for b in buckets: + b.write(r) +for b in buckets: + b.close() +f.close() + diff --git a/src/alignbucket.cpp b/src/alignbucket.cpp new file mode 100644 index 0000000..f6d115a --- /dev/null +++ b/src/alignbucket.cpp @@ -0,0 +1,386 @@ +/** + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation version 2.. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + + Authors: + - Giuseppe Profiti, + - Piero Fariselli, +*/ +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace std; +namespace po = boost::program_options; + +//Hypothesis about the numer of different lengths in the input +#define HYP_SIZE 35000 + +/** + * Reads a file containing the distribution of sequences by length. + * Each row in the file contains a length,a space and the number of proteins + * for that length. If a length is not present, its value for the number of + * proteins is automatically set to 0. + * @param filename the name of the file to read + * @param S the vector for the distribution (modified by this function) + * @param start the minimum length considered (associated to S[0]) + */ +void read_distr(const char* filename, vector* S, int start) { + unsigned int current; + unsigned int lastseed = start - 1; + long found = 0; + string line; + + ifstream myfile(filename, ios_base::in); + if (myfile.fail()) { + cerr << "ERROR: Can't open file " << filename << endl; + exit(-1); + } + if (myfile.is_open()) { + while (getline(myfile, line)) { + istringstream ss(line); + ss >> current; + ss >> found; + while (lastseed + 1 < current) { + S->push_back(0); + lastseed++; + } + if (current >= lastseed) { + S->push_back(found); + lastseed = current; + } + } + myfile.close(); + } +} + +/** + * Reads a fasta file and populates a vector with the distribution of proteins + * per length. Also returns a map of protein identifiers associated to lengths. + * @param filename the file to read + * @param S vector with length distribution (modified by this function) + * @param start minimum length to consider (associated to S[0]) + * @return a map of length->vector of identifiers + */ +map > read_fasta(const char* filename, vector* S, int start) { + map > res = map >(); + string line; + + ifstream myfile(filename, ios_base::in); + if (myfile.fail()) { + cerr << "ERROR: Can't open file " << filename << endl; + exit(-1); + } + if (myfile.is_open()) { + string lastseen = ""; + int count = 0; + while (getline(myfile, line)) { + if (line[0] == '>') { + if (lastseen.compare("") != 0) { + res[count].push_back(lastseen); + } + lastseen = line.substr(1); + count = 0; + } else { + count = count + line.size(); + } + } + res[count].push_back(lastseen); //the last one + } + myfile.close(); + + unsigned int current; + unsigned int lastseed = start - 1; + long found = 0; + for (std::map >::iterator it = res.begin(); it != res.end(); ++it) { + current = it->first; + found = it->second.size(); + while (lastseed + 1 < current) { + S->push_back(0); + lastseed++; + } + if (current >= lastseed) { + S->push_back(found); + lastseed = current; + } + } + return res; +} + +/** + * Cost function + * @param lower the lower bound (inclusive) + * @param upper the upper bound (inclusive) + * @param sumS vector of partial sums for the distribution + * @param sumsigma vector of partial sums for length*#elements of that length + * @return the cost of aligning sequences from lower to upper + */ +mpz_class cost(int lower, int upper, const vector &sumS, const vector &sumsigma) { + mpz_class isigma = sumsigma[upper]; + if (lower > 0) + isigma = isigma - sumsigma[lower - 1]; + mpz_class total = isigma * (sumS[upper] + 1); + if (lower > 0) + total = total - isigma * sumS[lower - 1]; + return total; +} + +/** + * The upper bound for a range + * @param i the "center" of the range + * @param maximum the upper bound of the domain + * @param delta the coverage ratio + * @return the upper bound for the range + */ +int upper(int i, int maximum,int delta) { + return min(int(floor(i / (delta/100.0))), maximum); +} + + +/** + * Evaluates the intervals identified by the algorithm + * @param lastpos the lastarray index to be used + * @param start the lower bound of lengths + * @param p the array of interval bounds + * @param length the length of array p + * @param delta the coverage ratio + * @return a vector of pairs representing the buckets + */ +vector > generate_intervals(int lastpos,int start, int p[], int length, int delta) +{ + int ll = max(p[lastpos] + start +1, start); + vector > intervals = vector >(); + int end = upper(lastpos + start,length-1+start,delta); + intervals.push_back(pair(ll,end)); + int i = p[lastpos]; + while ((ll > start) && (i>0)) { + ll = max(p[i] + start +1, start); + int end = upper(i + start, length - 1 + start,delta); + intervals.push_back(pair(ll,end)); + i = p[i]; + } + + return intervals; +} + + +/** + * Prints the intervals identified by the algorithm + * @param lastpos the lastarray index to be used + * @param start the lower bound of lengths + * @param p the array of interval bounds + * @param length the length of array p + * @param delta the coverage ratio + * @return a vector of pairs representing the buckets + */ +vector > print_intervals(vector > intervals) +{ + cout << "Intervals: " << endl; + for(std::vector >::iterator it = intervals.begin(); it != intervals.end(); ++it) + { + int ll = it->first; + int end = it->second; + cout << ll << ", " << end << endl; + } + + return intervals; +} + + +int main(int argc, const char* argv[]) { + vector S; + vector sumsigma, sumS; + S.reserve(HYP_SIZE); + //length -> identifiers + map > table; + int length; + int start = 1; + string outdir; + bool verbose = false; + int delta; + + // Declare the supported options. + po::options_description desc("Allowed options"); + desc.add_options() + ("help", "produce help message") + ("delta", po::value(&delta)->default_value(90), "Coverage percentage needed, please see the paper") + ("start,s", po::value(), "Minimum sequence length to consider") + ("distribution,d", po::value(), "file with length distribution. The content should be ") + ("fasta,f", po::value(), "file containing the sequences in FASTA format") + ("outdir", po::value(), "output directory") + ("verbose,v", "verbose mode. WARNING: may generate a huge amount of data") + ; + + po::variables_map vm; + po::store(po::parse_command_line(argc, argv, desc), vm); + po::notify(vm); + + if (vm.count("help")) { + cout << desc << "\n"; + return 1; + } + + if (vm.count("start")) { + start = vm["start"].as(); + cout << "Minimum length set to " + << start << ".\n"; + } else { + cout << "Using default minimum length: " << start << endl; + } + + if (vm.count("distribution")) { + string fname = vm["distribution"].as(); + cout << "Reading distribution file " + << fname << endl; + read_distr(fname.c_str(), &S, start); + cout << "Done reading." << endl; + } else if (vm.count("fasta")) { + string fname = vm["fasta"].as(); + cout << "Reading fasta file " + << fname << endl; + table = read_fasta(fname.c_str(), &S, start); + cout << "Done reading." << endl; + } else { + cout << "ERROR: please specify a distribution or a fasta file" << endl; + cout << desc << endl; + return 2; + } + + if (vm.count("outdir")) { + outdir = vm["outdir"].as(); + if (outdir[outdir.length()-1]!='/') + outdir.append("/"); + cout << "Output directory set to " + << outdir << endl; + } else { + outdir = "./"; + cout << "Output directory set to current working directory" << endl; + } + + if (vm.count("verbose")) { + verbose = true; + } + + + length = S.size(); + if (verbose) + cout << "Different lengths considered = " << length << endl; + sumsigma.resize(length); + sumS.resize(length); + + sumsigma[0] = start * S[0]; + sumS[0] = S[0]; + if (verbose) { + cout << "i\tS\tsumS\tsigma\tsumsigma" << endl; + cout << 0 << "\t" << sumS[0] << "\t" << sumsigma[0] << endl; + } + for (int i = 1; i < length; i++) { + sumS[i] = sumS[i - 1] + S[i]; + sumsigma[i] = sumsigma[i - 1]+(i + start) * S[i]; + if (verbose) + cout << i << "\t" << sumS[i] << "\t" << sumsigma[i] << endl; + } + + S.clear(); + + vector B; + int p[length]; + B.resize(length); + mpz_class naive = 0; + + ofstream outfile; + if (verbose) { + string ff = outdir+"matrix.csv"; + outfile.open(ff.c_str(), ios::out); + outfile << "i\tB\tp" << endl; + } + for (int i = 0; i < length; i++) { + int a = i + start; + int upper; + if (delta==100) + upper = min(a,length-1+start)-start; + else + upper = min(int(floor(a / (delta/100.0))), length - 1 + start) - start; + + mpz_class M = sumsigma[upper]*(sumS[upper] + 1); + p[i] = -1; + B[i] = M; + for (int k = 0; k <= i; k++) { + int lower = k-1; + M = cost(lower+1, upper, sumS, sumsigma); + if (B[i] > M + B[lower]) { + B[i] = M + B[lower]; + p[i] = lower; + } + } + if (delta==100) + naive = naive + cost(max(a,start)-start,upper,sumS,sumsigma); + else + naive = naive + cost(max(int(ceil(a * (delta/100.0))), start) - start, upper, sumS, sumsigma); + if (verbose) + outfile << i << "\t" << B[i] << "\t" << p[i] << endl; + } + + if (verbose) + outfile.close(); + + mpz_class tmptotal = 0; + + cout << "Naive partitioning cost=" << naive << " using " << length << " buckets" << endl; + cout << "Cost of full interval = " << cost(0, length - 1, sumS, sumsigma) << endl; + + sumsigma.clear(); + sumS.clear(); + + cout << "Minimum cost found = " << B[length - 1] << endl; + vector > intervals = generate_intervals(length-1,start, p, length, delta); + cout << "For a total of " << intervals. size() << " subsets" << endl; + if (verbose) + print_intervals(intervals); + + if (table.size()>0) + { // write the buckets to file + string fname = outdir+"buckets.list"; + ofstream bucket; + bucket.open(fname.c_str(), ios::out); + for(std::vector >::iterator it = intervals.begin(); it != intervals.end(); ++it) + { + int first = it->first; + int second = it->second; + + for(int i=first; i<=second; i++) + { + for(std::vector::iterator j=table[i].begin(); j!=table[i].end(); ++j) + { + bucket << *j << "\t" << first << "-" << second << endl; + } + } + } + bucket.close(); + } + + B.clear(); + + return 0; +}