Mercurial > repos > yufei-luo > s_mart
view commons/tools/dbConsensus.py @ 19:9bcfa7936eec
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:23:29 -0400 |
parents | 94ab73e8a190 |
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#!/usr/bin/env python # Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. import os import sys import getopt ##@file # usage: dbConsensus.py [ options ] # options: # -h: this help # -i: name of the input file (format=aligned fasta) # -n: minimum number of nucleotides in a column to edit a consensus (default=1) # -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0) # -o: name of the output file (default=inFileName+'.cons') # -v: verbose (default=0/1/2) if not os.environ.has_key( "REPET_PATH" ): print "ERROR: no environment variable REPET_PATH" sys.exit(1) sys.path.append( os.environ["REPET_PATH"] ) import commons.core.seq.AlignedBioseqDB def help(): """ Give the list of the command-line options. """ print print "usage:",sys.argv[0]," [ options ]" print "options:" print " -h: this help" print " -i: name of the input file (format=aligned fasta)" print " -n: minimum number of nucleotides in a column to edit a consensus (default=1)" print " -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0)" print " -o: name of the output file (default=inFileName+'.cons')" print " -H: format the header with pyramid and piles informations (SATannot)" print " -v: verbose (default=0/1/2)" print def main(): inFileName = "" minNbNt = 1 minPropNt = 0.0 outFileName = "" header_SATannot = False verbose = 0 try: opts, args = getopt.getopt(sys.argv[1:],"hi:n:p:o:v:H") except getopt.GetoptError, err: print str(err); help(); sys.exit(1) for o,a in opts: if o == "-h": help() sys.exit(0) elif o == "-i": inFileName = a elif o == "-n": minNbNt = int(a) elif o == "-p": minPropNt = float(a) elif o == "-o": outFileName = a elif o == "-H": header_SATannot = True elif o == "-v": verbose = int(a) if inFileName == "": print "ERROR: missing input file name" help() sys.exit(1) if verbose > 0: print "START %s" % (sys.argv[0].split("/")[-1]) sys.stdout.flush() alnDB = commons.core.seq.AlignedBioseqDB.AlignedBioseqDB( inFileName ) if alnDB.getSize() < minNbNt: print "WARNING: not enough sequences (<%i)" % ( minNbNt ) else: consensus = alnDB.getConsensus( minNbNt, minPropNt, verbose, header_SATannot) if consensus != None: consensus.upCase() if outFileName == "": outFileName = "%s.cons" % ( inFileName ) outFile = open( outFileName, "w" ) consensus.write( outFile ) outFile.close() if verbose > 0: print "END %s" % (sys.argv[0].split("/")[-1]) sys.stdout.flush() return 0 if __name__ == "__main__": main ()