Mercurial > repos > drosofff > msp_oases
comparison oases_optimiser.py @ 0:435711ba68e3 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Fri, 29 May 2015 12:41:13 -0400 |
| parents | |
| children | b4d1940ecc90 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:435711ba68e3 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 VelvetOptimiser Wrapper | |
| 5 refactored using the adaptation of | |
| 6 Konrad Paszkiewicz University of Exeter, UK. | |
| 7 | |
| 8 """ | |
| 9 import pkg_resources; | |
| 10 import logging, os, string, sys, tempfile, glob, shutil, types, urllib | |
| 11 import shlex, subprocess | |
| 12 from optparse import OptionParser, OptionGroup | |
| 13 from stat import * | |
| 14 | |
| 15 | |
| 16 def stop_err( msg ): | |
| 17 sys.stderr.write( "%s\n" % msg ) | |
| 18 sys.exit() | |
| 19 | |
| 20 def __main__(): | |
| 21 job_dir= os.getcwd() | |
| 22 #tmp_work_dir = tempfile.mkdtemp(dir = job_dir) # make temp directory in the job_dir | |
| 23 #Parse Command Line | |
| 24 starthash = sys.argv[1] | |
| 25 endhash = sys.argv[2] | |
| 26 inputs = sys.argv[3] | |
| 27 transcripts = sys.argv[4] | |
| 28 transcripts_path = '' | |
| 29 cmdline = "oases_optimiser.sh %s %s '%s' %s 2&1>/dev/null" % (starthash, endhash, inputs, job_dir) # 2&1>/dev/null | |
| 30 print >> sys.stdout, cmdline # so will appear as blurb for file | |
| 31 print >> sys.stdout, job_dir | |
| 32 print >> sys.stdout, "PATH = %s" % (os.environ['PATH']) | |
| 33 try: | |
| 34 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) # cwd=job_dir | |
| 35 returncode = proc.wait() | |
| 36 # get stderr, allowing for case where it's very large | |
| 37 stderr = '' | |
| 38 buffsize = 1048576 | |
| 39 try: | |
| 40 while True: | |
| 41 stderr += proc.stderr.read( buffsize ) | |
| 42 if not stderr or len( stderr ) % buffsize != 0: | |
| 43 break | |
| 44 except OverflowError: | |
| 45 pass | |
| 46 if returncode != 0: | |
| 47 raise Exception, stderr | |
| 48 except Exception, e: | |
| 49 stop_err( 'Error running oases_optimiser.py' + str( e ) ) | |
| 50 out = open(transcripts,'w') | |
| 51 transcript_path = os.path.join(job_dir, "MergedAssemblyFolder", 'transcripts.fa') | |
| 52 print >> sys.stdout, transcript_path | |
| 53 for line in open(transcript_path): | |
| 54 out.write( "%s" % (line) ) | |
| 55 out.close() | |
| 56 | |
| 57 if __name__ == "__main__": __main__() |