Mercurial > repos > drosofff > msp_oases

comparison oases_optimiser.py @ 2:b5df930313cc draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 22 Jun 2015 10:39:20 -0400
parents eedbe32980bb
children dc684e37f668
comparison
equal deleted inserted replaced
1:070f9de358fc 2:b5df930313cc
15 15
16 def stop_err( msg ): 16 def stop_err( msg ):
17 sys.stderr.write( "%s\n" % msg ) 17 sys.stderr.write( "%s\n" % msg )
18 sys.exit() 18 sys.exit()
19 19
20 def oases_optimiser(starthash, endhash, input, job_dir):
21 '''
22 Replaces call to oases_optimiser.sh. For all k-mers between
23 starthash and endhash run velvet and oases.
24 '''
25 for i in xrange(starthash, endhash, 2):
26 cmd1="velveth {0}/outputFolder_{1} {1} {2} && ".format(job_dir, i, input)
27 cmd2="velvetg {0}/outputFolder_{1} -read_trkg yes && ".format(job_dir, i)
28 cmd3="oases {0}/outputFolder_{1}".format(job_dir, i)
29 proc = subprocess.call( args=cmd1+cmd2+cmd3, shell=True, stdout=sys.stdout, stderr=sys.stderr )
30 cmd4="velveth {0}/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa && ".format(job_dir)
31 cmd5="velvetg {0}/MergedAssemblyFolder -read_trkg yes -conserveLong yes && ".format(job_dir)
32 cmd6="oases {0}/MergedAssemblyFolder -merge yes".format(job_dir)
33 proc = subprocess.call( args=cmd4+cmd5+cmd6, shell=True, stdout=sys.stdout, stderr=sys.stderr )
34
20 def __main__(): 35 def __main__():
21 job_dir= os.getcwd() 36 job_dir= os.getcwd()
22 #tmp_work_dir = tempfile.mkdtemp(dir = job_dir) # make temp directory in the job_dir
23 #Parse Command Line 37 #Parse Command Line
24 starthash = sys.argv[1] 38 starthash = int(sys.argv[1])
25 endhash = sys.argv[2] 39 endhash = int(sys.argv[2])
26 inputs = sys.argv[3] 40 input = sys.argv[3]
27 transcripts = sys.argv[4] 41 transcripts = sys.argv[4]
28 transcripts_path = '' 42 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']) 43 print >> sys.stdout, "PATH = %s" % (os.environ['PATH'])
33 try: 44 try:
34 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) # cwd=job_dir 45 oases_optimiser(starthash, endhash, input, 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: 46 except Exception, e:
49 stop_err( 'Error running oases_optimiser.py' + str( e ) ) 47 stop_err( 'Error running oases_optimiser.py' + str( e ) )
50 out = open(transcripts,'w') 48 out = open(transcripts,'w')
51 transcript_path = os.path.join(job_dir, "MergedAssemblyFolder", 'transcripts.fa') 49 transcript_path = os.path.join(job_dir, "MergedAssemblyFolder", 'transcripts.fa')
52 print >> sys.stdout, transcript_path 50 print >> sys.stdout, transcript_path