Mercurial > repos > drosofff > msp_oases

annotate oases_optimiser.py @ 0:435711ba68e3 draft

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