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7
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1 #!/usr/bin/env python
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2
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3
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4 import subprocess, tempfile, sys, os, glob, shutil, time, random
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5 from optparse import OptionParser
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6 from optparse import Option, OptionValueError
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7
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8 class VCFStorageWrapper(object):
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9
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10 def __init__(self):
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11 self._options = None
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12
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13
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14 def stop_err(self, msg ):
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15 sys.stderr.write( "%s\n" % msg )
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16 sys.exit()
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17
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18
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19 def setAttributesFromCmdLine(self):
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20 description = "VCFStorage_wrapper"
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21 description += "\nWrapper for VCFStorage\n VCFStorage "
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22 description += "VCFStorage stores info from variant calling into a table. It will create a tabulate file with the different infos\n"
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23 description += "example : VCFStorage -f fasta.fa -l genomelist.list -w workdir -o output.tab \n"
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24 parser = OptionParser(description = description, version = "0.1")
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25 parser.add_option("-f", "--fasta", dest = "fastaFile", action = "store", type = "string", help = "Input fasta file name [compulsory] [format: Fasta]", default = "")
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26 parser.add_option("-l", "--genomeNameList", dest = "genomeNameList", action = "append", type = "string", help = "Input list of genome name ")
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27 parser.add_option("-L", "--genomeFileList", dest = "genomeFileList", action = "append", type = "string", help = "Input list of genome VCF file ")
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28 parser.add_option("-w", "--workDir", dest = "workDir", action = "store", type = "string", help = "name of the workingDirectory", default = "")
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29 parser.add_option("-o", "--out", dest = "outFile", action = "store", type = "string", help = "Output file name [compulsory] [format: tab]", default = "")
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30 options = parser.parse_args()[0]
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31 self._setAttributesFromOptions(options)
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32
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33
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34 def _setAttributesFromOptions(self, options):
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35 self._options = options
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36
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37 def run(self):
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38 self.createGenomeList()
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39 cmd = self.createCmdLine()
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40 self.launchCmdLine(cmd)
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41
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42 def createGenomeList(self):
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43 self.genomelistFile = "%s.genomeListFile" % self._options.outFile
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44 lGenomeName = self._options.genomeNameList
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45 lGenomeVCF = self._options.genomeFileList
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46 output = open(self.genomelistFile, "w")
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47 for i,genomeName in enumerate(lGenomeName) :
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48 output.write("%s\t%s\n" % (lGenomeName[i],lGenomeVCF[i]))
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49 output.close()
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50
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51 def createCmdLine(self):
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52 workdir = "VCFStorage_%s_%d" % (time.strftime("%d%H%M%S"), random.randint(0, 10000))
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53 prg = "VCFStorage.py"
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54 args = ""
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55 args += "-f %s" % self._options.fastaFile
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56 args += " "
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57 args += "-o %s" % self._options.outFile
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58 args += " "
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59 args += "-l %s" % self.genomelistFile
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60 args += " "
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61 args += "-w %s" % workdir
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62 cmd = "%s %s" %(prg, args)
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63
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64 print cmd
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65 return cmd
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66
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67 def launchCmdLine(self, cmd):
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68 try:
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69 tmp_err = tempfile.NamedTemporaryFile().name
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70 tmp_stderr = open( tmp_err, 'wb' )
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71 proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
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72 returncode = proc.wait()
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73 tmp_stderr.close()
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74 # get stderr, allowing for case where it's very large
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75 tmp_stderr = open( tmp_err, 'rb' )
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76 stderr = ''
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77 buffsize = 1048576
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78 try:
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79 while True:
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80 stderr += tmp_stderr.read( buffsize )
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81 if not stderr or len( stderr ) % buffsize != 0:
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82 break
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83 except OverflowError:
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84 pass
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85 tmp_stderr.close()
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86 if stderr:
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87 raise Exception, stderr
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88 except Exception, e:
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89 os.remove(self.genomelistFile)
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90 self.stop_err( 'Error in VCFStorage:\n' + str( e ) )
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91 os.remove(self.genomelistFile)
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92
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93 if __name__ == "__main__":
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94 iWrapper = VCFStorageWrapper()
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95 iWrapper.setAttributesFromCmdLine()
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96 iWrapper.run()
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