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1 #! /usr/bin/env python
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2
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3 import os, sys, subprocess,tempfile
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4 from optparse import OptionParser
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5
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6 def stop_err(msg):
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7 sys.stderr.write('%s\n' % msg)
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8 sys.exit()
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9
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10 def __main__():
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11 #Parse Command Line
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12 description = "GMAP/GSNAP version:2012-12-20."
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13 parser = OptionParser(description = description)
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14 parser.add_option("-d", "--genomeName", dest="genomeName", help="Define the reference genome name.[compulsory]")
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15 parser.add_option("-o", "--outputFile", dest="outputfile", help="output[compulsory]")
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16 #parser.add_option("-D", "--workingDir", dest="workingdir", help="Define the directory of writing reference genome index.[compulsory]")
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17 parser.add_option("-k", "--kmer", dest="kmer", default=12, help="Choose kmer value (<=16), a big kmer value can take more RAM(4Go).[compulsory]")
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18 parser.add_option("-i", "--inputFasta", dest="inputFastaFile", help="Reference genome file, fasta format.[compulsory]")
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19 parser.add_option("-q", "--inputFastq", dest="inputFastqFile", help="Input fastq file.")
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20 parser.add_option("-p", "--pairedEnd", dest="pairedEndFile", default=None, help="Input paired-end fastq file.")
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21 parser.add_option("-A", "--outputFormat", dest="outputFormat", default="sam", help="Choose an output format [sam, goby (need to re-compile with appropriate options)].")
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22 (options, args) = parser.parse_args()
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23
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24 #If workingDir dose not exist, should create before run the job.
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25
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26 workingDir = os.path.dirname(options.inputFastaFile)
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27
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28 cmds = []
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29 cmd_setup = "gmap_setup -d %s -D %s -k %s %s" % (options.genomeName, workingDir, options.kmer, options.inputFastaFile)
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30 cmds.append(cmd_setup)
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31 cmd_make_coords = "make -f Makefile.%s coords" % options.genomeName
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32 cmds.append(cmd_make_coords)
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33 cmd_make_gmapdb = "make -f Makefile.%s gmapdb" % options.genomeName
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34 cmds.append(cmd_make_gmapdb)
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35 cmd_make_install = "make -f Makefile.%s install" % options.genomeName
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36 cmds.append(cmd_make_install)
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37 cmd_run = "gsnap -d %s -D %s -A %s %s " % (options.genomeName, workingDir, options.outputFormat, options.inputFastqFile)
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38 if options.pairedEndFile != None:
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39 cmd_run += "%s" % options.pairedEndFile
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40 cmd_run += " > %s" % options.outputfile
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41 cmds.append(cmd_run)
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42
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43 tmp_files = []
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44 for i in range(len(cmds)):
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45 try:
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46 tmp_out = tempfile.NamedTemporaryFile().name
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47 tmp_files.append(tmp_out)
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48 tmp_stdout = open(tmp_out, 'wb')
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49 tmp_err = tempfile.NamedTemporaryFile().name
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50 tmp_files.append(tmp_err)
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51 tmp_stderr = open(tmp_err, 'wb')
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52 proc = subprocess.Popen(args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr)
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53 returncode = proc.wait()
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54 tmp_stderr.close()
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55 #get stderr, allowing for case where it's very large
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56 tmp_stderr = open(tmp_err, 'rb')
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57 stderr = ''
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58 buffsize = 1048576
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59 try:
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60 while True:
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61 stderr += tmp_stderr.read(buffsize)
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62 if not stderr or len(stderr) % buffsize != 0:
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63 break
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64 except OverflowError:
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65 pass
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66 tmp_stdout.close()
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67 tmp_stderr.close()
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68 if returncode != 0:
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69 raise Exception, stderr
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70 except Exception, e:
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71 stop_err('Error in :\n' + str(e))
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72
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73 for tmp_file in tmp_files:
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74 os.remove(tmp_file)
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75
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76 if __name__=="__main__":__main__()
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