Mercurial > repos > drosofff > msp_oases

annotate oases_optimiser.py @ 4:42fad5f9c78e draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 4ea89b80296509604d1b224ee1671a6497ddca14
author drosofff
date Mon, 19 Oct 2015 11:56:34 -0400
parents b4d1940ecc90
children 58bf34f98232
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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 oases_optimiser(starthash, endhash, input, job_dir):
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21 '''
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22 Replaces call to oases_optimiser.sh. For all k-mers between
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23 starthash and endhash run velvet and oases.
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24 '''
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25 for i in xrange(starthash, endhash, 2):
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26 cmd1="velveth {0}/outputFolder_{1} {1} {2} && ".format(job_dir, i, input)
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27 cmd2="velvetg {0}/outputFolder_{1} -read_trkg yes && ".format(job_dir, i)
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28 cmd3="oases {0}/outputFolder_{1}".format(job_dir, i)
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29 proc = subprocess.call( args=cmd1+cmd2+cmd3, shell=True, stdout=sys.stdout, stderr=sys.stderr )
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30 cmd4="velveth {0}/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa && ".format(job_dir)
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31 cmd5="velvetg {0}/MergedAssemblyFolder -read_trkg yes -conserveLong yes && ".format(job_dir)
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32 cmd6="oases {0}/MergedAssemblyFolder -merge yes".format(job_dir)
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33 proc = subprocess.call( args=cmd4+cmd5+cmd6, shell=True, stdout=sys.stdout, stderr=sys.stderr )
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34
0
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35 def __main__():
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36 job_dir= os.getcwd()
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37 #Parse Command Line
3
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38 starthash = int(sys.argv[1])
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39 endhash = int(sys.argv[2])
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40 input = sys.argv[3]
0
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41 transcripts = sys.argv[4]
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42 transcripts_path = ''
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43 print >> sys.stdout, "PATH = %s" % (os.environ['PATH'])
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44 try:
3
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45 oases_optimiser(starthash, endhash, input, job_dir)
0
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46 except Exception, e:
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47 stop_err( 'Error running oases_optimiser.py' + str( e ) )
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48 out = open(transcripts,'w')
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49 transcript_path = os.path.join(job_dir, "MergedAssemblyFolder", 'transcripts.fa')
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50 print >> sys.stdout, transcript_path
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51 for line in open(transcript_path):
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52 out.write( "%s" % (line) )
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53 out.close()
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54
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55 if __name__ == "__main__": __main__()