comparison sopra_wpc.py @ 2:87ffe493b6c1 draft default tip

Use GALAXY_SLOTS for multithreading in Bowtie. Create symlinks instead of copying files. Specify in help that Bowtie is used to align the reads to the contigs. Add readme.rst .

1:d180348fe9db

    return result


def __main__():
    parser = optparse.OptionParser(description='SOPRA with prebuilt contigs')
    parser.add_option('--contigs', action='append', dest='contigs', help='Contigs FASTA files, at least 1')
    parser.add_option('--mate', action='append', dest='mates', help='Paired-end Illumina libraries, at least 1 FASTA file')
    parser.add_option('-d', action='append', dest='insert_sizes', type='int', help='List of insert sizes for the corresponding mate pair libraries')
    parser.add_option('-v', dest='max_mismatches', type='int', help='Maximum number of mismatches when aligning reads on contigs with Bowtie')
    parser.add_option('-c', dest='c_option', type='int', help='If the number of times a read and its reverse complement appear in the library is equal to or more than this value, the pairing information from that read will be disregarded')

        parser.error('Wrong number of arguments')

    contigs = options.contigs # a list of file paths
    mates = options.mates # a list of file paths
    insert_sizes = options.insert_sizes # a list of integers
    max_mismatches = options.max_mismatches
    c_option = options.c_option
    w_option = options.w_option
    L_option = options.L_option
    h_option = options.h_option
    scaffolds = options.scaffolds
    logfile = options.logfile

    s_scaf_path = which('s_scaf_v1.4.6.pl').pop()
    print 'Creating temp dir'
    wd = tempfile.mkdtemp()
    try:
        fake_mates = [os.path.join(wd, os.path.basename(mate) + '.fasta') for mate in mates] # s_prep_contigAseq_v1.4.6.pl wants a mate file with extension [Ff][Aa][Ss][Tt][Aa] or [Ff][Aa]
        contigs_sopra = os.path.join(wd, 'contigs_sopra.fasta') # s_prep_contigAseq_v1.4.6.pl always writes all the prepared contigs to this file
        bowtie_build = os.path.join(wd, 'bowtie_build') # arbitrary basename for bowtie-build output files
        mate_sopras = [os.path.splitext(fake_mate)[0] + '_sopra.fasta' for fake_mate in fake_mates] # s_prep_contigAseq_v1.4.6.pl writes the prepared paired reads to these files
        mysam_mates = [mate_sopra + '.sam' for mate_sopra in mate_sopras] # arbitrary filenames for bowtie output in SAM format
        mysam_mates_parsed = [mysam_mate + '_parsed' for mysam_mate in mysam_mates] # s_parse_sam_v1.4.6.pl writes its output to these files
        orientdistinfo = os.path.join(wd, 'orientdistinfo_c%d' % c_option) # s_read_parsed_sam_v1.4.6.pl writes its output to this file
        scaffolds_file = os.path.join(wd, "scaffolds_h%s_L%d_w%d.fasta" % (h_option, L_option, w_option)) # s_scaf_v1.4.6.pl writes its output to this file

        for i in range(len(mates)):
            print "Copying mate %s to %s" % (mates[i], fake_mates[i])
            shutil.copy2(mates[i], fake_mates[i])

        log = open(logfile, 'w') if logfile else sys.stdout
        try:
            cmd_step1 = "s_prep_contigAseq_v1.4.6.pl -contig %s -mate %s -a %s" % (" ".join(contigs), " ".join(fake_mates), wd)
            print "SOPRA with prebuilt contigs (preparation) command to be executed:\n %s" % cmd_step1

            cmd_step2 = "bowtie-build %s %s" % (contigs_sopra, bowtie_build)
            print "SOPRA with prebuilt contigs (Bowtie building index) command to be executed:\n %s" % cmd_step2
            subprocess.check_call(args=cmd_step2, stdout=log, shell=True)

            for i in range(len(mate_sopras)):
                cmd_step3 = "bowtie -v %d -m 1 -f --sam %s %s %s" % (max_mismatches, bowtie_build, mate_sopras[i], mysam_mates[i])
                print "SOPRA with prebuilt contigs (Bowtie alignment of library %d) command to be executed:\n %s" % (i+1, cmd_step3)
                subprocess.check_call(args=cmd_step3, stdout=log, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because bowtie writes some logging info there

            cmd_step4 = "s_parse_sam_v1.4.6.pl -sam %s -a %s" % (' '.join(mysam_mates), wd)
            print "SOPRA with prebuilt contigs (removing reads not mapped in a proper pair) command to be executed:\n %s" % cmd_step4

            subprocess.check_call(args=cmd_step6, stdout=log, shell=True)
        finally:
            if log != sys.stdout:
                log.close()

        print 'Moving result file %s to %s' % (scaffolds_file, scaffolds)
        shutil.move(scaffolds_file, scaffolds)
    finally:
        shutil.rmtree(wd)

2:87ffe493b6c1

    return result


def __main__():
    parser = optparse.OptionParser(description='SOPRA with prebuilt contigs')
    parser.add_option('-p', dest='num_threads', type='int', help='Number of threads for Bowtie')
    parser.add_option('--contigs', action='append', dest='contigs', help='Contigs FASTA files, at least 1')
    parser.add_option('--mate', action='append', dest='mates', help='Paired-end Illumina libraries, at least 1 FASTA file')
    parser.add_option('-d', action='append', dest='insert_sizes', type='int', help='List of insert sizes for the corresponding mate pair libraries')
    parser.add_option('-v', dest='max_mismatches', type='int', help='Maximum number of mismatches when aligning reads on contigs with Bowtie')
    parser.add_option('-c', dest='c_option', type='int', help='If the number of times a read and its reverse complement appear in the library is equal to or more than this value, the pairing information from that read will be disregarded')

        parser.error('Wrong number of arguments')

    contigs = options.contigs # a list of file paths
    mates = options.mates # a list of file paths
    insert_sizes = options.insert_sizes # a list of integers
    c_option = options.c_option
    w_option = options.w_option
    L_option = options.L_option
    h_option = options.h_option
    scaffolds = options.scaffolds
    logfile = options.logfile

    s_scaf_path = which('s_scaf_v1.4.6.pl').pop()
    print 'Creating temporary directory'
    wd = tempfile.mkdtemp()
    try:
        fake_mates = [os.path.join(wd, os.path.basename(mate) + '.fasta') for mate in mates] # s_prep_contigAseq_v1.4.6.pl wants a mate file with extension [Ff][Aa][Ss][Tt][Aa] or [Ff][Aa]
        contigs_sopra = os.path.join(wd, 'contigs_sopra.fasta') # s_prep_contigAseq_v1.4.6.pl always writes all the prepared contigs to this file
        bowtie_build = os.path.join(wd, 'bowtie_build') # arbitrary basename for bowtie-build output files
        mate_sopras = [os.path.splitext(fake_mate)[0] + '_sopra.fasta' for fake_mate in fake_mates] # s_prep_contigAseq_v1.4.6.pl writes the prepared paired reads to these files
        mysam_mates = [mate_sopra + '.sam' for mate_sopra in mate_sopras] # arbitrary filenames for bowtie output in SAM format
        mysam_mates_parsed = [mysam_mate + '_parsed' for mysam_mate in mysam_mates] # s_parse_sam_v1.4.6.pl writes its output to these files
        orientdistinfo = os.path.join(wd, "orientdistinfo_c%d" % c_option) # s_read_parsed_sam_v1.4.6.pl writes its output to this file
        scaffolds_file = os.path.join(wd, "scaffolds_h%s_L%d_w%d.fasta" % (h_option, L_option, w_option)) # s_scaf_v1.4.6.pl writes its output to this file

        for i in range(len(mates)):
            print "Creating symbolic link %s pointing to %s" % (fake_mates[i], mates[i])
            os.symlink(mates[i], fake_mates[i])

        log = open(logfile, 'w') if logfile else sys.stdout
        try:
            cmd_step1 = "s_prep_contigAseq_v1.4.6.pl -contig %s -mate %s -a %s" % (" ".join(contigs), " ".join(fake_mates), wd)
            print "SOPRA with prebuilt contigs (preparation) command to be executed:\n %s" % cmd_step1

            cmd_step2 = "bowtie-build %s %s" % (contigs_sopra, bowtie_build)
            print "SOPRA with prebuilt contigs (Bowtie building index) command to be executed:\n %s" % cmd_step2
            subprocess.check_call(args=cmd_step2, stdout=log, shell=True)

            for i in range(len(mate_sopras)):
                cmd_step3 = "bowtie -p %d -v %d -m 1 -f --sam %s %s %s" % (options.num_threads, options.max_mismatches, bowtie_build, mate_sopras[i], mysam_mates[i])
                print "SOPRA with prebuilt contigs (Bowtie alignment of library %d) command to be executed:\n %s" % (i+1, cmd_step3)
                subprocess.check_call(args=cmd_step3, stdout=log, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because bowtie writes some logging info there

            cmd_step4 = "s_parse_sam_v1.4.6.pl -sam %s -a %s" % (' '.join(mysam_mates), wd)
            print "SOPRA with prebuilt contigs (removing reads not mapped in a proper pair) command to be executed:\n %s" % cmd_step4

            subprocess.check_call(args=cmd_step6, stdout=log, shell=True)
        finally:
            if log != sys.stdout:
                log.close()

        print "Moving result file %s to %s" % (scaffolds_file, scaffolds)
        shutil.move(scaffolds_file, scaffolds)
    finally:
        shutil.rmtree(wd)