|
7
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3
|
|
|
4 import subprocess, tempfile, sys, os, glob, shutil, time
|
|
|
5 from optparse import OptionParser
|
|
|
6
|
|
|
7
|
|
|
8 class VCFCartoWrapper(object):
|
|
|
9
|
|
|
10 def __init__(self):
|
|
|
11 self._options = None
|
|
|
12
|
|
|
13
|
|
|
14 def stop_err(self, msg ):
|
|
|
15 sys.stderr.write( "%s\n" % msg )
|
|
|
16 sys.exit()
|
|
|
17
|
|
|
18
|
|
|
19 def setAttributesFromCmdLine(self):
|
|
|
20 description = "VCFcarto can convert your tabulated file into a file with only the SNP from refA and refH.\n"
|
|
|
21 description += "2 formats are possible, either the input format is conserved, or the format is changed into a 3 letter format\n"
|
|
|
22 description += "(\"A\" for refA, \"H\" for refH and \"-\" when the base do not correspond to any parent)\n\n"
|
|
|
23 description += "example 1 : VCFcarto.py -f Storage.out -A G15 -H G23 -o FilteredStorage.out\n"
|
|
|
24 description += "example 2 : VCFcarto.py -f Storage.out -A ref1 -H ref2 -p -s -g -m -o cartoTable.out\n"
|
|
|
25 parser = OptionParser(description = description, version = "0.1")
|
|
|
26 parser.add_option("-f", "--file", dest = "tableName", action = "store", type = "string", help = "Input TSV File name [compulsory] [format: TSV]", default = "")
|
|
|
27 parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output TSV File name [compulsory] [format: TSV]", default = "")
|
|
|
28 parser.add_option("-A", "--refA", dest = "refA", action = "store", type = "string", help = "name of the reference genome A [compulsory] ", default = "")
|
|
|
29 parser.add_option("-H", "--refH", dest = "refH", action = "store", type = "string", help = "name of the reference genome H [compulsory] ", default = "")
|
|
|
30 parser.add_option("-p", "--onlyParents", dest = "onlyPar", action = "store_true", help = "Will change every letters by either A or H depending on which parents the strain correspond to for that base[optional] [default: False]", default = False)
|
|
|
31 parser.add_option("-m", "--mergeMarkers", dest = "mergeMarkers", action = "store_true", help = "Will merge sequential markers with the same information ; option -p is needed [optional] [default: False]", default = False)
|
|
|
32 parser.add_option("-M", "--mergeFile", dest = "mergeFile", action = "store", type = "string", help = "name for the mergeFile ", default = "")
|
|
|
33 parser.add_option("-g", "--graphics", dest = "graphs", action = "store_true", help = "create graphs. Only works with -p[optional] [default: False]", default = False)
|
|
|
34 parser.add_option("-G", "--graphHTML", dest = "graphHTML", action = "store", type = "string", help = "name of the HTML linking to graphs ", default = "")
|
|
|
35 parser.add_option("-d", "--dirGraphs", dest = "dirGraphs", action = "store", type = "string", help = "name of the folder containing graphs ", default = "")
|
|
|
36 options = parser.parse_args()[0]
|
|
|
37 self._setAttributesFromOptions(options)
|
|
|
38
|
|
|
39
|
|
|
40 def _setAttributesFromOptions(self, options):
|
|
|
41 self._options = options
|
|
|
42
|
|
|
43 def run(self):
|
|
|
44 prg = "VCFCarto.py"
|
|
|
45 args = ""
|
|
|
46 args += "-f %s" % self._options.tableName
|
|
|
47 args += " "
|
|
|
48 args += "-o %s" % self._options.outFile
|
|
|
49 args += " "
|
|
|
50 args += "-A %s" % self._options.refA
|
|
|
51 args += " "
|
|
|
52 args += "-H %s" % self._options.refH
|
|
|
53 args += " "
|
|
|
54 args += "-v 2 "
|
|
|
55 if self._options.onlyPar :
|
|
|
56 args += " "
|
|
|
57 args += "-p"
|
|
|
58 if self._options.mergeMarkers :
|
|
|
59 args += " "
|
|
|
60 args += "-m"
|
|
|
61 if self._options.graphs :
|
|
|
62 args += " "
|
|
|
63 args += "-g"
|
|
|
64 cmd = "%s %s" %(prg, args)
|
|
|
65
|
|
|
66 print cmd
|
|
|
67
|
|
|
68 try:
|
|
|
69 tmp_err = tempfile.NamedTemporaryFile().name
|
|
|
70 tmp_stderr = open( tmp_err, 'wb' )
|
|
|
71 proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
|
|
|
72 returncode = proc.wait()
|
|
|
73 tmp_stderr.close()
|
|
|
74 # get stderr, allowing for case where it's very large
|
|
|
75 tmp_stderr = open( tmp_err, 'rb' )
|
|
|
76 stderr = ''
|
|
|
77 buffsize = 1048576
|
|
|
78 try:
|
|
|
79 while True:
|
|
|
80 stderr += tmp_stderr.read( buffsize )
|
|
|
81 if not stderr or len( stderr ) % buffsize != 0:
|
|
|
82 break
|
|
|
83 except OverflowError:
|
|
|
84 pass
|
|
|
85 tmp_stderr.close()
|
|
|
86 if stderr:
|
|
|
87 raise Exception, stderr
|
|
|
88 except Exception, e:
|
|
|
89 self.stop_err( 'Error in VCFCarto:\n' + str( e ) )
|
|
|
90
|
|
|
91 if self._options.mergeMarkers :
|
|
|
92 shutil.move("markerList.bed" ,self._options.mergeFile)
|
|
|
93 if self._options.graphs :
|
|
|
94 html = open(self._options.graphHTML, "w")
|
|
|
95
|
|
|
96 os.mkdir(self._options.dirGraphs)
|
|
|
97 lGraphsFiles = glob.glob("VCFCarto_graphs/*")
|
|
|
98 for file in lGraphsFiles :
|
|
|
99 baseName = os.path.basename(file)
|
|
|
100 shutil.move( file ,"%s/%s" %(self._options.dirGraphs, baseName))
|
|
|
101 line = "<img src=\"%s\" > \n" %(baseName)
|
|
|
102 html.write(line)
|
|
|
103
|
|
|
104 if __name__ == "__main__":
|
|
|
105 iWrapper = VCFCartoWrapper()
|
|
|
106 iWrapper.setAttributesFromCmdLine()
|
|
|
107 iWrapper.run()
|
