Mercurial > repos > ntino-krampis > viralcloud
comparison viral_assembly_annotation/VIGOR.py @ 0:beaf42837914 draft
viral cloud resource galaxy tool definitions initial commit
| author | ntino-krampis |
|---|---|
| date | Thu, 31 Jan 2013 13:41:35 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:beaf42837914 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Runs VIGOR3 on given input fasta file. | |
| 5 """ | |
| 6 | |
| 7 import os, sys, subprocess, tempfile, shutil | |
| 8 | |
| 9 def __main__(): | |
| 10 # Parse the command line options | |
| 11 (inputFasta,outputALN,outputCDS,outputFS,outputPEP,outputRPT,outputSTATS,outputTBL) = sys.argv[1:] | |
| 12 | |
| 13 # Set up output variables | |
| 14 outputDir = "/usr/local/VIGOR/tools/vigor/test" | |
| 15 outputName = "output" | |
| 16 outputLog = "%s/%s_log.txt" % (outputDir,outputName) | |
| 17 vigorOutputALN = "%s/%s.aln" % (outputDir,outputName) | |
| 18 vigorOutputCDS = "%s/%s.cds" % (outputDir,outputName) | |
| 19 vigorOutputFS = "%s/%s.fs" % (outputDir,outputName) | |
| 20 vigorOutputPEP = "%s/%s.pep" % (outputDir,outputName) | |
| 21 vigorOutputRPT = "%s/%s.rpt" % (outputDir,outputName) | |
| 22 vigorOutputSTATS = "%s/%s.stats" % (outputDir,outputName) | |
| 23 vigorOutputTBL = "%s/%s.tbl" % (outputDir,outputName) | |
| 24 | |
| 25 # Create empty output log file (cannot be created by VIGOR command alone). | |
| 26 os.system("sudo touch %s" % outputLog) | |
| 27 os.system("sudo chmod 777 %s" % outputLog) | |
| 28 | |
| 29 # Run command | |
| 30 command = "/usr/local/VIGOR/tools/vigor/prod3/VIGOR3.pl -A -i %s -O %s/%s > %s" % (inputFasta,outputDir,outputName,outputLog) | |
| 31 os.system("sudo %s" % command) | |
| 32 os.system("sudo chmod 777 %s/%s.*" % (outputDir,outputName)) | |
| 33 os.system("sudo cp %s %s" % (vigorOutputALN,outputALN)) | |
| 34 os.system("sudo cp %s %s" % (vigorOutputCDS,outputCDS)) | |
| 35 os.system("sudo cp %s %s" % (vigorOutputFS,outputFS)) | |
| 36 os.system("sudo cp %s %s" % (vigorOutputPEP,outputPEP)) | |
| 37 os.system("sudo cp %s %s" % (vigorOutputRPT,outputRPT)) | |
| 38 os.system("sudo cp %s %s" % (vigorOutputSTATS,outputSTATS)) | |
| 39 os.system("sudo cp %s %s" % (vigorOutputTBL,outputTBL)) | |
| 40 | |
| 41 if __name__=="__main__": | |
| 42 __main__() |