Mercurial > repos > drosofff > msp_oases

annotate oases_optimiser.py @ 5:58bf34f98232 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit 3d96056b65a38e7642cfeef4ed274dc76b88472a
author drosofff
date Fri, 29 Apr 2016 03:14:58 -0400
parents b4d1940ecc90
children
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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
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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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 os, sys
58bf34f98232 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit 3d96056b65a38e7642cfeef4ed274dc76b88472a
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10 import subprocess
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13 def stop_err(msg):
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14 sys.stderr.write("%s\n" % msg)
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15 sys.exit()
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18 def oases_optimiser(starthash, endhash, input):
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19 '''
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20 Replaces call to oases_optimiser.sh. For all k-mers between
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21 starthash and endhash run velvet and oases.
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22 '''
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23 for i in xrange(starthash, endhash, 2):
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24 cmd1 = "velveth outputFolder_{0} {0} {1} && ".format(i, input)
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25 cmd2 = "velvetg outputFolder_{0} -read_trkg yes && ".format(i)
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26 cmd3 = "oases outputFolder_{0}".format(i)
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27 proc = subprocess.call(args=cmd1 + cmd2 + cmd3, shell=True, stdout=sys.stdout, stderr=sys.stdout)
58bf34f98232 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit 3d96056b65a38e7642cfeef4ed274dc76b88472a
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28 if not proc == 0:
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29 print("Oases failed at k-mer %s, skipping" % i)
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30 continue
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31 cmd4 = "velveth MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa && "
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32 cmd5 = "velvetg MergedAssemblyFolder -read_trkg yes -conserveLong yes && "
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33 cmd6 = "oases MergedAssemblyFolder -merge yes"
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34 proc = subprocess.call(args=cmd4 + cmd5 + cmd6, shell=True, stdout=sys.stdout, stderr=sys.stdout)
58bf34f98232 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit 3d96056b65a38e7642cfeef4ed274dc76b88472a
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35 if not proc == 0:
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36 raise Exception("Oases could not merge assembly")
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38 def __main__():
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39 starthash = int(sys.argv[1])
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40 endhash = int(sys.argv[2])
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41 input = sys.argv[3]
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42 transcripts = sys.argv[4]
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43 try:
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44 oases_optimiser(starthash, endhash, input)
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45 except Exception, e:
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46 stop_err('Error running oases_optimiser.py\n' + str(e))
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47 with open(transcripts, 'w') as out:
58bf34f98232 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit 3d96056b65a38e7642cfeef4ed274dc76b88472a
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48 transcript_path = os.path.join("MergedAssemblyFolder", 'transcripts.fa')
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49 for line in open(transcript_path):
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50 out.write("%s" % (line))
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53 if __name__ == "__main__": __main__()