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1 # -*- coding: utf-8 -*-
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2 """
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3 SOPRA with prebuilt contigs workflow runner
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4 """
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5
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6 import optparse
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7 import os
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8 import tempfile
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9 import shutil
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10 import subprocess
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11 import sys
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12
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13
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14 # Copyright (c) Twisted Matrix Laboratories.
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15 def which(name, flags=os.X_OK):
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16 """ Search PATH for executable files with the given name. """
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17 result = []
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18 exts = filter(None, os.environ.get('PATHEXT', '').split(os.pathsep))
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19 path = os.environ.get('PATH', None)
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20 if path is None:
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21 return []
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22 for p in os.environ.get('PATH', '').split(os.pathsep):
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23 p = os.path.join(p, name)
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24 if os.access(p, flags):
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25 result.append(p)
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26 for e in exts:
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27 pext = p + e
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28 if os.access(pext, flags):
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29 result.append(pext)
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30 return result
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31
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32
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33 def __main__():
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34 parser = optparse.OptionParser(description='SOPRA with prebuilt contigs')
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35 parser.add_option('--contigs', action='append', dest='contigs', help='Contigs FASTA files, at least 1')
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36 parser.add_option('--mate', action='append', dest='mates', help='Paired-end Illumina libraries, at least 1 FASTA file')
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37 parser.add_option('-d', action='append', dest='insert_sizes', type='int', help='List of insert sizes for the corresponding mate pair libraries')
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38 parser.add_option('-v', dest='max_mismatches', type='int', help='Maximum number of mismatches when aligning reads on contigs with Bowtie')
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39 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')
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40 parser.add_option('-w', dest='w_option', type='int', help='Minimum number of links between two contigs')
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41 parser.add_option('-L', dest='L_option', type='int', help='Minimum length of contigs to be used in scaffold assembly')
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42 parser.add_option('--h_option', dest='h_option', type='float', help='High coverage contigs (above mean coverage + h x std coverage) are not considered in the scaffold assembly mainly to exclude reads from repetitive regions')
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43 parser.add_option('--scaffolds', dest='scaffolds', help='scaffolds fasta file mandatory')
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44 parser.add_option('-l', '--logfile', dest='logfile', help='log file (default=stdout)')
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45 (options, args) = parser.parse_args()
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46 if len(args) > 0:
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47 parser.error('Wrong number of arguments')
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48
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49 contigs = options.contigs # a list of file paths
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50 mates = options.mates # a list of file paths
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51 insert_sizes = options.insert_sizes # a list of integers
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52 max_mismatches = options.max_mismatches
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53 c_option = options.c_option
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54 w_option = options.w_option
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55 L_option = options.L_option
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56 h_option = options.h_option
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57 scaffolds = options.scaffolds
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58 logfile = options.logfile
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59
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60 s_scaf_path = which('s_scaf_v1.4.6.pl').pop()
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61 print 'Creating temp dir'
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62 wd = tempfile.mkdtemp()
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63 try:
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64 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]
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65 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
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66 bowtie_build = os.path.join(wd, 'bowtie_build') # arbitrary basename for bowtie-build output files
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67 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
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68 mysam_mates = [mate_sopra + '.sam' for mate_sopra in mate_sopras] # arbitrary filenames for bowtie output in SAM format
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69 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
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70 orientdistinfo = os.path.join(wd, 'orientdistinfo_c%d' % c_option) # s_read_parsed_sam_v1.4.6.pl writes its output to this file
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71 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
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72
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73 for i in range(len(mates)):
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74 print "Copying mate %s to %s" % (mates[i], fake_mates[i])
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75 shutil.copy2(mates[i], fake_mates[i])
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76
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77 log = open(logfile, 'w') if logfile else sys.stdout
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78 try:
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79 cmd_step1 = "s_prep_contigAseq_v1.4.6.pl -contig %s -mate %s -a %s" % (" ".join(contigs), " ".join(fake_mates), wd)
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80 print "SOPRA with prebuilt contigs (preparation) command to be executed:\n %s" % cmd_step1
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81 subprocess.check_call(args=cmd_step1, stdout=log, shell=True)
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82
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83 cmd_step2 = "bowtie-build %s %s" % (contigs_sopra, bowtie_build)
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84 print "SOPRA with prebuilt contigs (Bowtie building index) command to be executed:\n %s" % cmd_step2
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85 subprocess.check_call(args=cmd_step2, stdout=log, shell=True)
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86
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87 for i in range(len(mate_sopras)):
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88 cmd_step3 = "bowtie -v %d -m 1 -f --sam %s %s %s" % (max_mismatches, bowtie_build, mate_sopras[i], mysam_mates[i])
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89 print "SOPRA with prebuilt contigs (Bowtie alignment of library %d) command to be executed:\n %s" % (i+1, cmd_step3)
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90 subprocess.check_call(args=cmd_step3, stdout=log, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because bowtie writes some logging info there
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91
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92 cmd_step4 = "s_parse_sam_v1.4.6.pl -sam %s -a %s" % (' '.join(mysam_mates), wd)
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93 print "SOPRA with prebuilt contigs (removing reads not mapped in a proper pair) command to be executed:\n %s" % cmd_step4
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94 subprocess.check_call(args=cmd_step4, stdout=log, shell=True)
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95
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96 cmd_step5 = "s_read_parsed_sam_v1.4.6.pl -c %d -a %s" % (c_option, wd)
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97 for i in range(len(mysam_mates_parsed)):
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98 cmd_step5 += " -parsed %s -d %d" % (mysam_mates_parsed[i], insert_sizes[i])
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99 print "SOPRA with prebuilt contigs (read parsed SAM) command to be executed:\n %s" % cmd_step5
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100 subprocess.check_call(args=cmd_step5, stdout=log, shell=True)
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101
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102 cmd_step6 = "perl -X %s -w %d -L %d -h %s -o %s -a %s" % (s_scaf_path, w_option, L_option, h_option, orientdistinfo, wd) # need to call with perl -X because: 1) otherwise some Perl warnings are written on stderr; 2) simply redirecting stderr would hide real errors since it always returns exit status 0
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103 print "SOPRA with prebuilt contigs (scaffold assembly) command to be executed:\n %s" % cmd_step6
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104 subprocess.check_call(args=cmd_step6, stdout=log, shell=True)
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105 finally:
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106 if log != sys.stdout:
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107 log.close()
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108
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109 print 'Moving result file %s to %s' % (scaffolds_file, scaffolds)
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110 shutil.move(scaffolds_file, scaffolds)
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111 finally:
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112 shutil.rmtree(wd)
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113
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114
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115 if __name__ == "__main__":
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116 __main__()
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