Mercurial > repos > cmonjeau > commet

comparison commet.py @ 3:d085f995d556

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remove prepare_commet and change/add packages
author cmonjeau
date Thu, 10 Sep 2015 13:38:21 +0000
parents a6beb4d4c417
children a53ce9294c0a
comparison
equal deleted inserted replaced
2:1478d48df8c7 3:d085f995d556
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import sys, tempfile, subprocess, glob 2 import sys, tempfile, subprocess, glob
3 import os, re, shutil, optparse 3 import os, re, shutil, argparse
4 import zipfile, tarfile, gzip 4 import zipfile, tarfile, gzip
5 from os.path import basename 5 from os.path import basename
6 6
7 """ 7 """
8 WARNING : 8 WARNING :
11 11
12 commet is available after compiling sources : 12 commet is available after compiling sources :
13 13
14 http://github.com/pierrepeterlongo/commet 14 http://github.com/pierrepeterlongo/commet
15 15
16 or with the galaxy_commet package in the GenOuest toolshed (coming soon) 16 or with the package_commet package in the GenOuest toolshed and the main toolshed
17 17
18 NOTE : 18 NOTE :
19 19
20 please add the line #!/usr/bin/env python in top of the Commet.py file if you've a bash error. 20 please add the line #!/usr/bin/env python in top of the Commet.py file if you've a bash error.
21 21
23 """ 23 """
24 24
25 def __main__(): 25 def __main__():
26 26
27 # arguments recuperation 27 # arguments recuperation
28 parser = optparse.OptionParser() 28 parser = argparse.ArgumentParser()
29 parser.add_option("--input", dest="input")
30 parser.add_option("-k", dest="kmer")
31 parser.add_option("-t", dest="minsharedkmer")
32 parser.add_option("-l", dest="minlengthread")
33 parser.add_option("-n", dest="maxn")
34 parser.add_option("-e", dest="minshannonindex")
35 parser.add_option("-m", dest="maxreads")
36 29
37 parser.add_option("--output") 30 parser.add_argument("--set", dest="set", action='append')
38 parser.add_option("--output_vectors") 31 parser.add_argument("-k", dest="kmer")
39 parser.add_option("--output_dendro") 32 parser.add_argument("-t", dest="minsharedkmer")
40 parser.add_option("--output_logs") 33 parser.add_argument("-l", dest="minlengthread")
41 parser.add_option("--output_matrix") 34 parser.add_argument("-n", dest="maxn")
42 parser.add_option("--output_heatmap1") 35 parser.add_argument("-e", dest="minshannonindex")
43 parser.add_option("--output_heatmap2") 36 parser.add_argument("-m", dest="maxreads")
44 parser.add_option("--output_heatmap3")
45 37
46 (options, args) = parser.parse_args() 38 parser.add_argument("--output")
39 parser.add_argument("--output_vectors")
40 parser.add_argument("--output_dendro")
41 parser.add_argument("--output_matrix")
42 parser.add_argument("--output_heatmap1")
43 parser.add_argument("--output_heatmap2")
44 parser.add_argument("--output_heatmap3")
47 45
46 options = parser.parse_args()
48 47
49 # copy R script into the current dir 48 # copy R script into the current dir
50 shutil.copy(os.environ['RSCRIPTS']+"/heatmap.r", os.getcwd()) 49 shutil.copy(os.environ['RSCRIPTS']+"/heatmap.r", os.getcwd())
51 shutil.copy(os.environ['RSCRIPTS']+"/dendro.R", os.getcwd()) 50 shutil.copy(os.environ['RSCRIPTS']+"/dendro.R", os.getcwd())
52 51
53 # remove the first line of the input file 52 # prepare input file
54 commet_file = open(options.input, "r") 53 commet_file=open('commet_config_file', 'w')
55 commet_file_clean = open("commet_clean_file", "w") 54
56 55 for set in options.set:
57 # delete the first line 56 clean_set=set.replace(',', ';').replace('::', ':')
58 commet_file.readline() 57 commet_file.write(clean_set+"\n")
59 for line in commet_file: 58 commet_file.close()
60 commet_file_clean.write(line)
61
62 # close files
63 commet_file.close()
64 commet_file_clean.close()
65 59
66 # edit the command line 60 # edit the command line
67 cmd_line=[] 61 cmd_line=[]
68 cmd_line.append("Commet.py") 62 cmd_line.append("Commet.py")
69 cmd_line.extend(["commet_clean_file","-b",os.environ['BINARIES'],"-k",options.kmer,"-t",options.minsharedkmer,"-l",options.minlengthread,"-e",options.minshannonindex]) 63 cmd_line.extend(["commet_config_file","-b",os.environ['BINARIES'],"-k",options.kmer,"-t",options.minsharedkmer,"-l",options.minlengthread,"-e",options.minshannonindex])
70 64
71 # add options 65 # add options
72 if options.maxn: 66 if options.maxn:
73
74 #cmd_line += ' -n '+options.maxn+' -m '+options.maxreads+' > '+options.output+' 2>>'+options.output
75 cmd_line.extend(["-n",options.maxn,"-m",options.maxreads]) 67 cmd_line.extend(["-n",options.maxn,"-m",options.maxreads])
76 #else:
77 #cmd_line += ' > '+options.output+' 2>>'+options.output
78 68
79 # execute job 69 # execute job
80 p=subprocess.Popen(cmd_line, 70 p=subprocess.call(cmd_line)
81 stdout=subprocess.PIPE,stderr=subprocess.PIPE)
82 71
83 stdoutput, stderror = p.communicate() 72 print "[COMMAND LINE]"+' '.join(cmd_line)
84
85 # log file
86 logfile=open(options.output, "w")
87 logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
88 logfile.write(str(stdoutput))
89 logfile.write(str(stderror))
90 logfile.close()
91 73
92 # copy .bv files inside a .bv archive 74 # copy .bv files inside a .bv archive
93 tmp_output_dir=os.getcwd()+"/output_commet/" 75 tmp_output_dir=os.getcwd()+"/output_commet/"
94 os.chdir(tmp_output_dir) 76 os.chdir(tmp_output_dir)
95 77
118 shutil.move(tmp_output_dir+'bv.zip.temp', options.output_vectors) 100 shutil.move(tmp_output_dir+'bv.zip.temp', options.output_vectors)
119 shutil.move(tmp_output_dir+'log.zip.temp', options.output_logs) 101 shutil.move(tmp_output_dir+'log.zip.temp', options.output_logs)
120 shutil.move(tmp_output_dir+'matrix.zip.temp', options.output_matrix) 102 shutil.move(tmp_output_dir+'matrix.zip.temp', options.output_matrix)
121 103
122 # outputs 104 # outputs
123 shutil.move(tmp_output_dir+'dendrogram_normalized.png', options.output_dendro) 105 try:
124 shutil.move(tmp_output_dir+'heatmap_normalized.png', options.output_heatmap1) 106 shutil.move(tmp_output_dir+'dendrogram_normalized.png', options.output_dendro)
125 shutil.move(tmp_output_dir+'heatmap_percentage.png', options.output_heatmap2) 107 shutil.move(tmp_output_dir+'heatmap_percentage.png', options.output_heatmap2)
126 shutil.move(tmp_output_dir+'heatmap_plain.png', options.output_heatmap3) 108 shutil.move(tmp_output_dir+'heatmap_normalized.png', options.output_heatmap1)
109 shutil.move(tmp_output_dir+'heatmap_plain.png', options.output_heatmap3)
110 except:
111 print "There is a problem with gplots execution"
127 112
128 if __name__ == "__main__": __main__() 113 if __name__ == "__main__": __main__()
129 114