Mercurial > repos > artbio > oases
view oases_optimiser.py @ 0:f7dd852c8f4c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
author | artbio |
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date | Sun, 15 Oct 2017 19:07:38 -0400 |
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#!/usr/bin/env python """ VelvetOptimiser Wrapper refactored using the adaptation of Konrad Paszkiewicz University of Exeter, UK. """ import os import subprocess import sys def stop_err(msg): sys.stderr.write("%s\n" % msg) sys.exit() def oases_optimiser(starthash, endhash, input): ''' Replaces call to oases_optimiser.sh. For all k-mers between starthash and endhash run velvet and oases. ''' for i in range(starthash, endhash, 2): cmd1 = "velveth outputFolder_{0} {0} {1} && ".format(i, input) cmd2 = "velvetg outputFolder_{0} -read_trkg yes && ".format(i) cmd3 = "oases outputFolder_{0}".format(i) proc = subprocess.call(args=cmd1 + cmd2 + cmd3, shell=True, stdout=sys.stdout, stderr=sys.stdout) if not proc == 0: print("Oases failed at k-mer %s, skipping" % i) continue cmd4 = "velveth MergedAssemblyFolder 27 -long\ outputFolder_*/transcripts.fa && " cmd5 = "velvetg MergedAssemblyFolder -read_trkg yes -conserveLong yes && " cmd6 = "oases MergedAssemblyFolder -merge yes" proc = subprocess.call(args=cmd4 + cmd5 + cmd6, shell=True, stdout=sys.stdout, stderr=sys.stdout) if not proc == 0: raise Exception("Oases could not merge assembly") def __main__(): starthash = int(sys.argv[1]) endhash = int(sys.argv[2]) input = sys.argv[3] transcripts = sys.argv[4] try: oases_optimiser(starthash, endhash, input) except Exception as e: stop_err('Error running oases_optimiser.py\n' + str(e)) with open(transcripts, 'w') as out: transcript_path = os.path.join('MergedAssemblyFolder', 'transcripts.fa') for line in open(transcript_path): out.write("%s" % (line)) if __name__ == "__main__": __main__()