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1 import sys, tempfile, subprocess, glob
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2 import os, re, shutil, stat
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3 import optparse
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4 from os.path import basename
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5
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6 """
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7
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8 Created by Cyril Monjeaud
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9 Cyril.Monjeaud@irisa.fr
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10 Modified by Fabrice Legeai
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11 fabrice.legeai@rennes.inra.fr
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12
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13 Last modifications : 04/21/2015
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14
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15 WARNING :
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16
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17 discoSNP++.py needs:
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18
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19 - run_discoSnp++.sh
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20 - discoSNP++_to_genotypes.py
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21 - the build repository next to the scripts
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22
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23 All these files are available after compiling the sources of discoSNP :
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24
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25 https://colibread.inria.fr/files/2013/10/DiscoSNPpp-2.0.6-Source.zip
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26
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27 or with the package_discoSnp_plus_plus package in the toolshed
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28
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29 """
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30
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31
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32 def __main__():
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33
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34 # store inputs in an array
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35 parser = optparse.OptionParser()
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36 parser.add_option("-r", dest="data_files")
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37 parser.add_option("-b", dest="branching_bubbles")
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38 parser.add_option("-D", dest="deletions")
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39 parser.add_option("-P", dest="min_snps")
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40 parser.add_option("-l", action="store_true", dest="low_complexity")
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41 parser.add_option("-k", dest="kmer")
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42 parser.add_option("-t", action="store_true", dest="left_right_unitigs")
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43 parser.add_option("-T", action="store_true", dest="left_right_contigs")
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44 parser.add_option("-c", dest="coverage")
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45 parser.add_option("-C", dest="maxcoverage")
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46 parser.add_option("-d", dest="error_threshold")
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47 parser.add_option("-n", action="store_true", dest="genotypes")
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48 parser.add_option("-G", dest="reference")
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49 parser.add_option("-M", dest="mapping_error")
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50
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51 (options, args) = parser.parse_args()
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52
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53 # create the working dir inside job_working_dir
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54 output_dir = os.mkdir("job_outputs")
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55
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56 cmd_line=[]
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57 cmd_line.append("/bin/bash")
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58 #cmd_line.append("/home/genouest/inrarennes/flegeai/local/DiscoSNP/DiscoSNP++-2.1.4-Source/run_discoSnp++.sh")
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59 cmd_line.append("run_discoSnp++.sh")
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60 #cmd_line.append("-B /local/bwa/bwa-0.7.10/")
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61
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62 # transform .dat into .fasta or .fastq for kissreads2
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63 link_files=[]
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64 f = open(options.data_files, 'r')
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65 files = f.readlines()
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66 for file in files:
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67 file=file.strip()
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68 if re.search("^$",file): continue
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69 tagfile=[]
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70 tagfile=re.split('::', file)
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71 number = int(tagfile[0])+1
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72 if re.search("^>.*", open(tagfile[1]).readline()):
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73 link_file = 'input'+str(number)+'.fasta'
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74 else:
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75 link_file = 'input'+str(number)+'.fastq'
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76
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77 os.symlink(tagfile[1], link_file)
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78 link_files.append(link_file)
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79
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80
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81 # edit the command line
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82 cmd_line.extend(["-r",' '.join(link_files),"-b",options.branching_bubbles,"-D",options.deletions,"-P",options.min_snps,"-k",options.kmer,"-c",options.coverage,"-C",options.maxcoverage,"-d",options.error_threshold])
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83 if options.low_complexity:
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84 cmd_line.append("-l")
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85 if options.left_right_unitigs:
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86 cmd_line.append("-t")
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87 if options.left_right_contigs:
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88 cmd_line.append("-T")
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89 if options.genotypes:
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90 cmd_line.append("-n")
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91
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92 # genotype part
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93 if options.reference:
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94 cmd_line.extend(["-G", options.reference])
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95 cmd_line.extend(["-M", options.mapping_error])
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96
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97 cmd_line.extend(["-p","job_outputs/galaxy"])
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98
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99 # execute job
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100 p=subprocess.Popen(cmd_line,
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101 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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102
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103 stdoutput, stderror = p.communicate()
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104
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105 # report file
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106 logfile=open("report.txt", "w")
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107 logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
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108 logfile.write(stdoutput)
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109
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110 # print stderror because it's informations
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111 logfile.write(stderror)
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112
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113 # close logfile
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114 logfile.close()
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115
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116 # change .fa extension to .fasta for a correct print inside Galaxy
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117 fafiles = glob.glob("job_outputs/*_coherent.fa")
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118 for fafile in fafiles:
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119 shutil.move(fafile, "coherent.fasta")
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120 vcffiles = glob.glob("job_outputs/*_coherent.vcf")
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121 for vcffile in vcffiles:
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122 shutil.move(vcffile, "coherent.vcf")
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123
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124
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125 if __name__ == "__main__": __main__()
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126
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