view commons/launcher/LaunchBlastclust.py @ 31:0ab839023fe4

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#!/usr/bin/env python

"""
Launch Blastclust on nucleotide sequences and return a fasta file.
"""

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
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# modify and/ or redistribute the software under the terms of the CeCILL
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# "http://www.cecill.info". 
#
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import os
import sys
import subprocess
from commons.core.seq.BioseqDB import BioseqDB
from commons.core.seq.Bioseq import Bioseq
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders

class LaunchBlastclust(object):
    """
    Launch Blastclust on nucleotide sequences and return a fasta file.
    """
    
    def __init__(self, input = "", outFilePrefix = "", clean = False, verbose = 0):
        """
        Constructor.
        """
        self._inFileName = input
        self._identityThreshold = 95
        self._coverageThreshold = 0.9
        self._bothSeq = "T"
        self._filterUnclusteredSeq = False
        self._outFilePrefix = outFilePrefix
        self._isBlastToMap = False
        self._isHeaderForTEdenovo = False
        self._nbCPUs = 1
        self._clean = clean
        self._verbose = verbose
        self._tmpFileName = ""
        
    def setAttributesFromCmdLine(self):
        """
        Set the attributes from the command-line.
        """
        
        description = "Launch Blastclust on nucleotide sequences and return a fasta file."
        usage = "LaunchBlastclust.py -i inputFileName [options]"
        
        examples = "\nExample 1: launch Blastclust with default options, highest verbose and clean temporary files.\n"
        examples += "\t$ python ./LaunchBlastclust.py -i MyBank.fa -v 2 -c"
        examples += "\n\t"
        examples += "\t\nExample 2: launch Blastclust with an identity threshold of 90%, rename output files and generate a map file corresponding to the fasta output.\n"
        examples += "\t$ python ./LaunchBlastclust.py -i MyBank.fa -S 90 -o SpecialOutputName -m"
        examples += "\n\tWARNING: Please refer to -m option limitations in the description above.\n"
        
        #TODO: check if the optionParser can handle '\' into strings for a better code readability in -m option
        
        parser = RepetOptionParser(description = description, usage = usage, version = "v1.0", epilog = examples)
        parser.add_option("-i", "--input",          dest = "inFileName",            type = "string",    help = "name of the input fasta file (nucleotides)",                    default = "")
        parser.add_option("-L", "--length",         dest = "coverageThreshold",     type = "float",     help = "length coverage threshold (default=0.9)",                       default = 0.9)
        parser.add_option("-S", "--ident",          dest = "identityThreshold",     type = "int",       help = "identity threshold (default=95)",                               default = 95)
        parser.add_option("-b", "--both",           dest = "bothSeq",               type = "string",    help = "require coverage on both neighbours (default=T/F)",             default = "T")
        parser.add_option("-f", "--filter",         dest = "filterUnclusteredSeq",                      help = "filter unclustered sequences",                                  default = False,    action="store_true")
        parser.add_option("-o", "--out",            dest = "outFilePrefix",         type = "string",    help = "prefix of the output files (default=input fasta file name)",    default = "")
        parser.add_option("-m", "--map",            dest = "isBlast2Map",                               help = "generate an additional output file in map format (Warning: only works if blastclust's fasta input headers are formated like LTRharvest fasta output)",   default = False,    action="store_true")
        parser.add_option("", "--TEdenovoHeader",   dest = "isHeaderForTEdenovo",                       help = "format headers for TEdenovo pipeline",                          default = False,    action="store_true")
        parser.add_option("-n", "--num",            dest = "nbCPUs",                type = "int",       help = "number of CPU's to use (default=1)",                            default = 1)
        parser.add_option("-c", "--clean",          dest = "clean",                                     help = "clean temporary files",                                         default = False,    action="store_true")
        parser.add_option("-v", "--verbose",        dest = "verbose",               type = "int",       help = "verbosity level (default=0/1/2)",                               default = 0)

        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setInputFileName(options.inFileName)
        self.setCoverageThreshold(options.coverageThreshold)
        self.setIdentityThreshold(options.identityThreshold)
        self.setBothSequences(options.bothSeq)
        self.setNbCPUs(options.nbCPUs)
        self.setIsHeaderForTEdenovo(options.isHeaderForTEdenovo)
        if options.filterUnclusteredSeq:
            self.setFilterUnclusteredSequences()
        if options.outFilePrefix != "":
            self.setOutputFilePrefix(options.outFilePrefix)
        else:
            self._outFilePrefix = self._inFileName
        if options.isBlast2Map:
            self.setIsBlastToMap()
        if options.clean:
            self.setClean()
        self.setVerbosityLevel(options.verbose)
                
    def setInputFileName(self , inFileName):
        self._inFileName = inFileName
        
    def setCoverageThreshold(self, lengthThresh):
        self._coverageThreshold = float(lengthThresh)
                
    def setIdentityThreshold(self, identityThresh):
        self._identityThreshold = int(identityThresh)
        
    def setBothSequences(self, bothSeq):
        self._bothSeq = bothSeq
        
    def setNbCPUs(self, nbCPUs):
        self._nbCPUs = int(nbCPUs)
        
    def setFilterUnclusteredSequences(self):
        self._filterUnclusteredSeq = True
        
    def setOutputFilePrefix(self, outFilePrefix):
        self._outFilePrefix = outFilePrefix
        
    def setIsBlastToMap(self):
        self._isBlastToMap = True
        
    def setIsHeaderForTEdenovo(self, isHeaderForTEdenovo):
        self._isHeaderForTEdenovo = isHeaderForTEdenovo
        
    def setClean(self):
        self._clean = True
        
    def setVerbosityLevel(self, verbose):
        self._verbose = int(verbose)
    
    def setTmpFileName(self, tmpFileName):    
        self._tmpFileName = tmpFileName
        
        
    def checkAttributes(self):
        """
        Check the attributes are valid before running the algorithm.
        """
        if self._inFileName == "":
            print "ERROR: missing input file name (-i)"
            sys.exit(1)
        if self._outFilePrefix == "":
            self._outFilePrefix = self._inFileName
        self._tmpFileName = "%s_blastclust.txt" % (self._outFilePrefix)
        
        
    def launchBlastclust(self, inFile):
        """
        Launch Blastclust in command-line.
        """
        if os.path.exists(os.path.basename(inFile)):
            inFile = os.path.basename(inFile)
        prg = "blastclust"
        cmd = prg
        cmd += " -i %s" % (inFile)
        cmd += " -o %s" % (self._tmpFileName)
        cmd += " -S %i" % (self._identityThreshold)
        cmd += " -L %f" % (self._coverageThreshold)
        cmd += " -b %s" % (self._bothSeq)
        cmd += " -p F"
        cmd += " -a %i" % (self._nbCPUs)
        if self._verbose == 0:
            cmd += " -v blastclust.log"
        if self._verbose > 0:
            print cmd
            sys.stdout.flush()
        process = subprocess.Popen(cmd, shell = True)
        process.communicate()
        if process.returncode != 0:
            raise Exception("ERROR when launching '%s'" % cmd)
        if self._clean and os.path.exists("error.log"):
            os.remove("error.log")
        if self._clean and os.path.exists("blastclust.log"):
            os.remove("blastclust.log")
            
            
    def getClustersFromTxtFile(self):
        """
        Return a dictionary with cluster IDs as keys and sequence headers as values.
        """
        dClusterId2SeqHeaders = {}
        inF = open(self._tmpFileName, "r")
        line = inF.readline()
        clusterId = 1
        while True:
            if line == "":
                break
            tokens = line[:-1].split(" ")
            dClusterId2SeqHeaders[clusterId] = []
            for seqHeader in tokens:
                if seqHeader != "":
                    dClusterId2SeqHeaders[clusterId].append(seqHeader)
            line = inF.readline()
            clusterId += 1
        inF.close()
        if self._verbose > 0:
            print "nb of clusters: %i" % (len(dClusterId2SeqHeaders.keys()))
            sys.stdout.flush()
        return dClusterId2SeqHeaders
    
    
    def filterUnclusteredSequences(self, dClusterId2SeqHeaders):
        """
        Filter clusters having only one sequence.
        """
        for clusterId in dClusterId2SeqHeaders.keys():
            if len(dClusterId2SeqHeaders[clusterId]) == 1:
                del dClusterId2SeqHeaders[clusterId]
        if self._verbose > 0:
            print "nb of clusters (>1seq): %i" % (len(dClusterId2SeqHeaders.keys()))
            sys.stdout.flush()
        return dClusterId2SeqHeaders
    
    
    def getClusteringResultsInFasta(self, inFile):
        """
        Write a fasta file whose sequence headers contain the clustering IDs.
        """
        dClusterId2SeqHeaders = self.getClustersFromTxtFile()
        if self._filterUnclusteredSeq:
            dClusterId2SeqHeaders = self.filterUnclusteredSequences(dClusterId2SeqHeaders)
        inDB = BioseqDB(inFile)
        outFileName = "%s_Blastclust.fa" % (inFile)
        outF = open(outFileName, "w")
        for clusterId in dClusterId2SeqHeaders.keys():
            memberId = 1
            for seqHeader in dClusterId2SeqHeaders[clusterId]:
                bs = inDB.fetch(seqHeader)
                bs.header = "BlastclustCluster%iMb%i_%s" % (clusterId, memberId, seqHeader)
                bs.write(outF)
                memberId += 1
        outF.close()
        
        
    def getLinkInitNewHeaders(self):
        dNew2Init = {}
        linkFileName = "%s.shortHlink" % (self._inFileName)
        linkFile = open(linkFileName,"r")
        line = linkFile.readline()
        while True:
            if line == "":
                break
            data = line.split("\t")
            dNew2Init[data[0]] = data[1]
            line = linkFile.readline()
        linkFile.close()
        return dNew2Init
    
    
    def retrieveInitHeaders(self, dNewH2InitH):
        tmpFaFile = "%s.shortH_Blastclust.fa" % (self._inFileName)
        tmpFaFileHandler = open(tmpFaFile, "r")
        outFaFile = "%s_Blastclust.fa" % (self._outFilePrefix)
        outFaFileHandler = open(outFaFile, "w")
        while True:
            line = tmpFaFileHandler.readline()
            if line == "":
                break
            if line[0] == ">":
                tokens = line[1:-1].split("_")
                initHeader = dNewH2InitH[tokens[1]]
                if self._isHeaderForTEdenovo:
                    classif = initHeader.split("_")[0]
                    consensusName = "_".join(initHeader.split("_")[1:])
                    clusterId = tokens[0].split("Cluster")[1].split("Mb")[0]
                    newHeader = "%s_Blc%s_%s" % (classif, clusterId, consensusName)
                else:
                    newHeader = "%s_%s" % (tokens[0], initHeader)
                outFaFileHandler.write(">%s\n" % (newHeader))
            else:
                outFaFileHandler.write(line)
        tmpFaFileHandler.close()
        outFaFileHandler.close()
        if self._clean:
            os.remove(tmpFaFile)


    def blastclustToMap(self, blastclustFastaOut):
        """
        Write a map file from blastclust fasta output.
        Warning: only works if blastclust's fasta input headers are formated like LTRharvest fasta output.
        """
        fileDb = open(blastclustFastaOut , "r")
        mapFilename = "%s.map" % (os.path.splitext(blastclustFastaOut)[0])
        fileMap = open(mapFilename, "w")
        seq = Bioseq()
        numseq = 0
        while 1:
            seq.read(fileDb)
            if seq.sequence == None:
                break
            numseq = numseq + 1
            ID = seq.header.split(' ')[0].split('_')[0]
            chunk = seq.header.split(' ')[0].split('_')[1]
            start = seq.header.split(' ')[-1].split(',')[0][1:]
            end = seq.header.split(' ')[-1].split(',')[1][:-1]
            line= '%s\t%s\t%s\t%s' % (ID, chunk, start, end)
            fileMap.write(line + "\n")
    
        fileDb.close()
        fileMap.close()
        print "saved in %s" % mapFilename 
        
        
    def start(self):
        """
        Useful commands before running the program.
        """
        self.checkAttributes()
        if self._verbose > 0:
            print "START %s" % (type(self).__name__)
            
            
    def end(self):
        """
        Useful commands before ending the program.
        """
        if self._verbose > 0:
            print "END %s" % (type(self).__name__)
            
            
    def run(self):
        """
        Run the program.
        """
        self.start()
        
        iCSH = ChangeSequenceHeaders(inFile = self._inFileName, format = "fasta", step = 1, outFile = "%s.shortH" % self._inFileName, linkFile = "%s.shortHlink" % self._inFileName)
        iCSH.run()
        
        self.launchBlastclust("%s.shortH" % (self._inFileName))
        
        self.getClusteringResultsInFasta("%s.shortH" % (self._inFileName))
        
        dNewH2InitH = self.getLinkInitNewHeaders()
        self.retrieveInitHeaders(dNewH2InitH)
        
        if self._isBlastToMap:
            blastclustFileName = "%s_Blastclust.fa" % (self._outFilePrefix)
            self.blastclustToMap(blastclustFileName)
        
        if self._clean:
            os.remove("%s.shortH" % (self._inFileName))
            os.remove("%s.shortHlink" % (self._inFileName))
        
        self.end()
        
if __name__ == "__main__":
    i = LaunchBlastclust()
    i.setAttributesFromCmdLine()
    i.run()