Mercurial > repos > urgi-team > vcfgandalftools
diff VCFCarto_wrapper.py @ 0:3552a8d9f51c draft
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author | urgi-team |
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date | Tue, 10 Nov 2015 08:30:56 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFCarto_wrapper.py Tue Nov 10 08:30:56 2015 -0500 @@ -0,0 +1,107 @@ +#!/usr/bin/env python + + +import subprocess, tempfile, sys, os, glob, shutil, time +from optparse import OptionParser + + +class VCFCartoWrapper(object): + + def __init__(self): + self._options = None + + + def stop_err(self, msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + + + def setAttributesFromCmdLine(self): + description = "VCFcarto can convert your tabulated file into a file with only the SNP from refA and refH.\n" + description += "2 formats are possible, either the input format is conserved, or the format is changed into a 3 letter format\n" + description += "(\"A\" for refA, \"H\" for refH and \"-\" when the base do not correspond to any parent)\n\n" + description += "example 1 : VCFcarto.py -f Storage.out -A G15 -H G23 -o FilteredStorage.out\n" + description += "example 2 : VCFcarto.py -f Storage.out -A ref1 -H ref2 -p -s -g -m -o cartoTable.out\n" + parser = OptionParser(description = description, version = "0.1") + parser.add_option("-f", "--file", dest = "tableName", action = "store", type = "string", help = "Input TSV File name [compulsory] [format: TSV]", default = "") + parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output TSV File name [compulsory] [format: TSV]", default = "") + parser.add_option("-A", "--refA", dest = "refA", action = "store", type = "string", help = "name of the reference genome A [compulsory] ", default = "") + parser.add_option("-H", "--refH", dest = "refH", action = "store", type = "string", help = "name of the reference genome H [compulsory] ", default = "") + 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) + 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) + parser.add_option("-M", "--mergeFile", dest = "mergeFile", action = "store", type = "string", help = "name for the mergeFile ", default = "") + parser.add_option("-g", "--graphics", dest = "graphs", action = "store_true", help = "create graphs. Only works with -p[optional] [default: False]", default = False) + parser.add_option("-G", "--graphHTML", dest = "graphHTML", action = "store", type = "string", help = "name of the HTML linking to graphs ", default = "") + parser.add_option("-d", "--dirGraphs", dest = "dirGraphs", action = "store", type = "string", help = "name of the folder containing graphs ", default = "") + options = parser.parse_args()[0] + self._setAttributesFromOptions(options) + + + def _setAttributesFromOptions(self, options): + self._options = options + + def run(self): + prg = "VCFCarto.py" + args = "" + args += "-f %s" % self._options.tableName + args += " " + args += "-o %s" % self._options.outFile + args += " " + args += "-A %s" % self._options.refA + args += " " + args += "-H %s" % self._options.refH + args += " " + args += "-v 2 " + if self._options.onlyPar : + args += " " + args += "-p" + if self._options.mergeMarkers : + args += " " + args += "-m" + if self._options.graphs : + args += " " + args += "-g" + cmd = "%s %s" %(prg, args) + + print cmd + + try: + tmp_err = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_err, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp_err, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if stderr: + raise Exception, stderr + except Exception, e: + self.stop_err( 'Error in VCFCarto:\n' + str( e ) ) + + if self._options.mergeMarkers : + shutil.move("markerList.bed" ,self._options.mergeFile) + if self._options.graphs : + html = open(self._options.graphHTML, "w") + + os.mkdir(self._options.dirGraphs) + lGraphsFiles = glob.glob("VCFCarto_graphs/*") + for file in lGraphsFiles : + baseName = os.path.basename(file) + shutil.move( file ,"%s/%s" %(self._options.dirGraphs, baseName)) + line = "<img src=\"%s\" > \n" %(baseName) + html.write(line) + +if __name__ == "__main__": + iWrapper = VCFCartoWrapper() + iWrapper.setAttributesFromCmdLine() + iWrapper.run()