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1 #!/usr/bin/env python
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2 import sys, tempfile, subprocess, glob
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3
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3 import os, re, shutil, argparse
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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 package_commet package in the GenOuest toolshed and the main toolshed
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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 = argparse.ArgumentParser()
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29
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30 parser.add_argument("--set", dest="set", action='append')
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31 parser.add_argument("-k", dest="kmer")
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32 parser.add_argument("-t", dest="minsharedkmer")
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33 parser.add_argument("-l", dest="minlengthread")
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34 parser.add_argument("-n", dest="maxn")
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35 parser.add_argument("-e", dest="minshannonindex")
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36 parser.add_argument("-m", dest="maxreads")
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37
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38 parser.add_argument("--output")
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39 parser.add_argument("--output_vectors")
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40 parser.add_argument("--output_dendro")
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41 parser.add_argument("--output_matrix")
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42 parser.add_argument("--output_heatmap1")
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43 parser.add_argument("--output_heatmap2")
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44 parser.add_argument("--output_heatmap3")
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45
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46 options = parser.parse_args()
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47
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48 # copy R script into the current dir
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49 shutil.copy(os.environ['RSCRIPTS']+"/heatmap.r", os.getcwd())
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50 shutil.copy(os.environ['RSCRIPTS']+"/dendro.R", os.getcwd())
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51
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52 # prepare input file
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53 commet_file=open('commet_config_file', 'w')
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54
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55 for set in options.set:
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56 clean_set=set.replace(',', ';').replace('::', ':')
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57 commet_file.write(clean_set+"\n")
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58 commet_file.close()
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59
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60 # edit the command line
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61 cmd_line=[]
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62 cmd_line.append("Commet.py")
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63 cmd_line.extend(["commet_config_file","-b",os.environ['BINARIES'],"-k",options.kmer,"-t",options.minsharedkmer,"-l",options.minlengthread,"-e",options.minshannonindex])
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64
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65 # add options
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66 if options.maxn:
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67 cmd_line.extend(["-n",options.maxn,"-m",options.maxreads])
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68
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69 # execute job
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70 p=subprocess.call(cmd_line)
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71
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72 print "[COMMAND LINE]"+' '.join(cmd_line)
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73
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74 # copy .bv files inside a .bv archive
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75 tmp_output_dir=os.getcwd()+"/output_commet/"
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76 os.chdir(tmp_output_dir)
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77
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78 # create zip outputs
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79 mybvzipfile=zipfile.ZipFile(tmp_output_dir+'bv.zip.temp', 'w')
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80 mylogzipfile=zipfile.ZipFile(tmp_output_dir+'log.zip.temp', 'w')
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81 mymatrixzipfile=zipfile.ZipFile(tmp_output_dir+'matrix.zip.temp', 'w')
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82
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83 # write files into the specific archive
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84 list_files = glob.glob(tmp_output_dir+'/*')
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85 for i in list_files:
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86
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87 if re.search("\.bv$", i):
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88 mybvzipfile.write(os.path.basename(i))
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89 if re.search("\.log$", i):
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90 mylogzipfile.write(os.path.basename(i))
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91 if re.search(".csv$", i):
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92 mymatrixzipfile.write(os.path.basename(i))
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93
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94 # close zip files
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95 mybvzipfile.close()
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96 mylogzipfile.close()
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97 mymatrixzipfile.close()
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98
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99 # return the archives
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100 shutil.move(tmp_output_dir+'bv.zip.temp', options.output_vectors)
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101 shutil.move(tmp_output_dir+'log.zip.temp', options.output_logs)
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102 shutil.move(tmp_output_dir+'matrix.zip.temp', options.output_matrix)
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103
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104 # outputs
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105 try:
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106 shutil.move(tmp_output_dir+'dendrogram_normalized.png', options.output_dendro)
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107 shutil.move(tmp_output_dir+'heatmap_percentage.png', options.output_heatmap2)
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108 shutil.move(tmp_output_dir+'heatmap_normalized.png', options.output_heatmap1)
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109 shutil.move(tmp_output_dir+'heatmap_plain.png', options.output_heatmap3)
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110 except:
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111 print "There is a problem with gplots execution"
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112
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113 if __name__ == "__main__": __main__()
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114
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