annotate SMART/Java/Python/WrappGetDistribution.py @ 24:452e051f6562

Deleted selected files

1 #! /usr/bin/env python
2 from optparse import OptionParser
3 import tarfile
4 import os
5 import re
6 import shutil
7 import subprocess
8 
9 SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
10 
11 def toTar(tarFileName, directory):
12     fileName = os.path.splitext(tarFileName)[0]
13     fileNameBaseName = os.path.basename(fileName)
14     tfile = tarfile.open(fileName + ".tmp.tar", "w")
15     list = os.listdir(directory)
16     for file in list:
17         if re.search(str(fileNameBaseName), file):
18             tfile.add(file)
19     os.system("mv %s %s" % (fileName + ".tmp.tar", options.outTarFileName))
20     tfile.close()
21     
22 
23 if __name__ == "__main__":
24     
25     magnifyingFactor = 1000
26     
27     # parse command line
28     description = "Get Distribution v1.0.1: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"
29 
30     parser = OptionParser(description = description)
31     parser.add_option("-i", "--input",       dest="inputFileName",     action="store",                     type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
32     parser.add_option("-f", "--format",      dest="format",            action="store",                     type="string", help="format of the input file [compulsory] [format: transcript file format]")
33     parser.add_option("-o", "--output",      dest="outTarFileName",    action="store",                     type="string", help="output file [compulsory] [format: output file in GFF3 format]")
34     parser.add_option("-r", "--reference",   dest="referenceFileName", action="store",      default=None,  type="string", help="file containing the genome [compulsory] [format: file in FASTA format]")
35     parser.add_option("-n", "--nbBins",      dest="nbBins",            action="store",      default=1000,  type="int",    help="number of bins [default: 1000] [format: int]")
36     parser.add_option("-2", "--bothStrands", dest="bothStrands",       action="store_true", default=False,                help="plot one curve per strand [format: bool] [default: false]")
37     parser.add_option("-w", "--raw",         dest="raw",               action="store_true", default=False,                help="plot raw number of occurrences instead of density [format: bool] [default: false]")
38     parser.add_option("-x", "--csv",         dest="csv",               action="store_true", default=False,                help="write a .csv file [format: bool]")
39     parser.add_option("-c", "--chromosome",  dest="chromosome",        action="store",      default=None,  type="string", help="plot only a chromosome [format: string]")
40     parser.add_option("-s", "--start",       dest="start",             action="store",      default=None,  type="int",    help="start from a given region [format: int]")
41     parser.add_option("-e", "--end",         dest="end",               action="store",      default=None,  type="int",    help="end from a given region [format: int]")
42     parser.add_option("-y", "--yMin",        dest="yMin",              action="store",      default=None,  type="int",    help="minimum value on the y-axis to plot [format: int]")
43     parser.add_option("-Y", "--yMax",        dest="yMax",              action="store",      default=None,  type="int",    help="maximum value on the y-axis to plot [format: int]")
44     parser.add_option("-g", "--gff",         dest="gff",               action="store_true", default=False,                help="also write GFF3 file [format: bool] [default: false]")
45     parser.add_option("-H", "--height",      dest="height",            action="store",      default=None,  type="int",    help="height of the graphics [format: int] [default: 300]")
46     parser.add_option("-W", "--width",       dest="width",             action="store",      default=None,  type="int",    help="width of the graphics [format: int] [default: 1000]")
47     parser.add_option("-v", "--verbosity",   dest="verbosity",         action="store",      default=1,     type="int",    help="trace level [default: 1] [format: int]")
48     parser.add_option("-l", "--log",         dest="log",               action="store_true", default=False,                help="write a log file [format: bool]")
49     (options, args) = parser.parse_args()
50 
51 
52     absPath = os.getcwd()
53     print "the current path is :", absPath
54     directory = "/tmp/wrappGetDistribution"
55     print "the dir path is :", directory
56     if not os.path.exists(directory):
57         os.makedirs(directory)
58     os.chdir(directory)
59     if options.inputFileName != None and options.format != None and options.outTarFileName != None:
60         outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0]
61         cmd = "python %s/Java/Python/getDistribution.py -i %s -f %s -o %s -D %s" % (SMART_PATH, options.inputFileName, options.format, outputFileName, directory)
62     if options.referenceFileName != None :
63         cmd += " -r %s" % options.referenceFileName
64     if options.nbBins != None :
65         cmd += " -n %s" % options.nbBins
66     if options.chromosome :
67         cmd += " -c %s" % options.chromosome 
68     if options.start != None :
69         cmd += " -s %s" % options.start
70     if options.end != None :
71         cmd += " -e %s" % options.end
72     if options.yMin != None :
73         cmd += " -y %s" % options.yMin
74     if options.yMax != None :
75         cmd += " -Y %s" % options.yMax
76     if options.height != None :
77         cmd += " -H %s" % options.height
78     if options.width != None :
79         cmd += " -W %s" % options.width
80     if options.bothStrands :
81         cmd += " -2" 
82     if options.raw :
83         cmd += " -w" 
84     if options.csv :
85         cmd += " -x" 
86     if options.gff :
87         cmd += " -g"
88     if options.log :
89         cmd += " -l" 
90     print "cmd is: ", cmd    
91     status = subprocess.call(cmd, shell=True)
92     if status != 0:
93             raise Exception("Problem with the execution of command!")
94     toTar(options.outTarFileName, directory)
95     shutil.rmtree(directory)
96