Mercurial > repos > xuebing > sharplabtool
view tools/ilmn_pacbio/assembly_stats.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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#!/usr/bin/env python # #Copyright (c) 2011, Pacific Biosciences of California, Inc. # #All rights reserved. # #Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: # * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. # * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. # #THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED #WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY #DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; #LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT #(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # import sys, os from optparse import OptionParser from galaxy import eggs import pkg_resources pkg_resources.require( 'bx-python' ) from bx.seq.fasta import FastaReader def getStats( fastaFile, genomeLength, minContigLength ): lengths = [] stats = { "Num" : 0, "Sum" : 0, "Max" : 0, "Avg" : 0, "N50" : 0, "99%" : 0 } fasta_reader = FastaReader( open( fastaFile, 'rb' ) ) while True: seq = fasta_reader.next() if not seq: break if seq.length < minContigLength: continue lengths.append( seq.length ) if lengths: stats[ 'Num' ] = len( lengths ) stats[ 'Sum' ] = sum( lengths ) stats[ 'Max' ] = max( lengths ) stats[ 'Avg' ] = int( sum( lengths ) / float( len( lengths ) ) ) stats[ 'N50' ] = 0 stats[ '99%' ] = 0 if genomeLength == 0: genomeLength = sum( lengths ) lengths.sort() lengths.reverse() lenSum = 0 stats[ "99%" ] = len( lengths ) for idx, length in enumerate( lengths ): lenSum += length if ( lenSum > genomeLength / 2 ): stats[ "N50" ] = length break lenSum = 0 for idx, length in enumerate( lengths ): lenSum += length if lenSum > genomeLength * 0.99: stats[ "99%" ] = idx + 1 break return stats def __main__(): #Parse Command Line usage = 'Usage: %prog input output --minContigLength' parser = OptionParser( usage=usage ) parser.add_option( "--minContigLength", dest="minContigLength", help="Minimum length of contigs to analyze" ) parser.add_option( "--genomeLength", dest="genomeLength", help="Length of genome for which to calculate N50s" ) parser.set_defaults( minContigLength=0, genomeLength=0 ) options, args = parser.parse_args() input_fasta_file = args[ 0 ] output_tabular_file = args[ 1 ] statKeys = "Num Sum Max Avg N50 99%".split( " " ) stats = getStats( input_fasta_file, int( options.genomeLength ), int( options.minContigLength ) ) fout = open( output_tabular_file, "w" ) fout.write( "%s\n" % "\t".join( map( lambda key: str( stats[ key ] ), statKeys ) ) ) fout.close() if __name__=="__main__": __main__()