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1 #!/usr/bin/env python
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2 import sys, tempfile, subprocess, glob
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3 import os, re, shutil, optparse
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4 import zipfile, tarfile, gzip
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5 from os.path import basename
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6
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7 """
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8 WARNING :
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9
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10 commet.py needs commet_exe binaries in your $PATH
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11
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12 commet is available after compiling sources :
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13
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14 http://github.com/pierrepeterlongo/commet
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15
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16 or with the galaxy_commet package in the GenOuest toolshed (coming soon)
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17
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18 NOTE :
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19
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20 please add the line #!/usr/bin/env python in top of the Commet.py file if you've a bash error.
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21
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22
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23 """
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24
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25 def __main__():
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26
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27 # arguments recuperation
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28 parser = optparse.OptionParser()
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29 parser.add_option("--input", dest="input")
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30 parser.add_option("-k", dest="kmer")
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31 parser.add_option("-t", dest="minsharedkmer")
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32 parser.add_option("-l", dest="minlengthread")
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33 parser.add_option("-n", dest="maxn")
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34 parser.add_option("-e", dest="minshannonindex")
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35 parser.add_option("-m", dest="maxreads")
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36
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37 parser.add_option("--output")
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38 parser.add_option("--output_vectors")
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39 parser.add_option("--output_dendro")
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40 parser.add_option("--output_logs")
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41 parser.add_option("--output_matrix")
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42 parser.add_option("--output_heatmap1")
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43 parser.add_option("--output_heatmap2")
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44 parser.add_option("--output_heatmap3")
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45
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46 (options, args) = parser.parse_args()
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47
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48
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49 # copy R script into the current dir
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50 shutil.copy(os.environ['RSCRIPTS']+"/heatmap.r", os.getcwd())
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51 shutil.copy(os.environ['RSCRIPTS']+"/dendro.R", os.getcwd())
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52
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53 # remove the first line of the input file
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54 commet_file = open(options.input, "r")
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55 commet_file_clean = open("commet_clean_file", "w")
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56
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57 # delete the first line
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58 commet_file.readline()
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59 for line in commet_file:
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60 commet_file_clean.write(line)
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61
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62 # close files
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63 commet_file.close()
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64 commet_file_clean.close()
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65
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66 # edit the command line
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67 cmd_line=[]
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68 cmd_line.append("Commet.py")
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69 cmd_line.extend(["commet_clean_file","-b",os.environ['BINARIES'],"-k",options.kmer,"-t",options.minsharedkmer,"-l",options.minlengthread,"-e",options.minshannonindex])
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70
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71 # add options
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72 if options.maxn:
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73
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74 #cmd_line += ' -n '+options.maxn+' -m '+options.maxreads+' > '+options.output+' 2>>'+options.output
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75 cmd_line.extend(["-n",options.maxn,"-m",options.maxreads])
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76 #else:
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77 #cmd_line += ' > '+options.output+' 2>>'+options.output
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78
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79 # execute job
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80 p=subprocess.Popen(cmd_line,
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81 stdout=subprocess.PIPE,stderr=subprocess.PIPE)
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82
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83 stdoutput, stderror = p.communicate()
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84
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85 # log file
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86 logfile=open(options.output, "w")
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87 logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
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88 logfile.write(str(stdoutput))
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89 logfile.write(str(stderror))
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90 logfile.close()
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91
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92 # copy .bv files inside a .bv archive
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93 tmp_output_dir=os.getcwd()+"/output_commet/"
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94 os.chdir(tmp_output_dir)
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95
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96 # create zip outputs
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97 mybvzipfile=zipfile.ZipFile(tmp_output_dir+'bv.zip.temp', 'w')
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98 mylogzipfile=zipfile.ZipFile(tmp_output_dir+'log.zip.temp', 'w')
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99 mymatrixzipfile=zipfile.ZipFile(tmp_output_dir+'matrix.zip.temp', 'w')
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100
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101 # write files into the specific archive
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102 list_files = glob.glob(tmp_output_dir+'/*')
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103 for i in list_files:
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104
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105 if re.search("\.bv$", i):
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106 mybvzipfile.write(os.path.basename(i))
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107 if re.search("\.log$", i):
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108 mylogzipfile.write(os.path.basename(i))
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109 if re.search(".csv$", i):
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110 mymatrixzipfile.write(os.path.basename(i))
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111
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112 # close zip files
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113 mybvzipfile.close()
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114 mylogzipfile.close()
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115 mymatrixzipfile.close()
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116
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117 # return the archives
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118 shutil.move(tmp_output_dir+'bv.zip.temp', options.output_vectors)
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119 shutil.move(tmp_output_dir+'log.zip.temp', options.output_logs)
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120 shutil.move(tmp_output_dir+'matrix.zip.temp', options.output_matrix)
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121
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122 # outputs
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123 shutil.move(tmp_output_dir+'dendrogram_normalized.png', options.output_dendro)
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124 shutil.move(tmp_output_dir+'heatmap_normalized.png', options.output_heatmap1)
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125 shutil.move(tmp_output_dir+'heatmap_percentage.png', options.output_heatmap2)
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126 shutil.move(tmp_output_dir+'heatmap_plain.png', options.output_heatmap3)
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127
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128 if __name__ == "__main__": __main__()
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129
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