Mercurial > repos > urgi-team > gandalfworkflow
comparison VCFCarto_wrapper.py @ 7:a6b557df86db draft
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author | urgi-team |
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date | Tue, 15 Dec 2015 05:35:36 -0500 |
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6:7557b71a92e7 | 7:a6b557df86db |
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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() |