def main(args): parser = OptionParser('usage: %prog [options]') optionsAvailable = ( ('-i', '--input', 'inputfile', 'string'), ('-o', '--output', 'outputfile', 'string'), ('-s', '--sequencefileid', 'Sequence_File_ID', 'int'), ) for oa in optionsAvailable: parser.add_option(oa[0], oa[1], dest=oa[2], type=oa[3]) (options, args) = parser.parse_args(args) outfn = options.outputfile.replace('.fasta','') out, rc = runCommand((FASTA_FILTER_PATH, '-r0.4', '-H18', '-a:4', '-A0', '--output=%s' % outfn, options.inputfile), True) if rc != 0: raise Exception readsC, sequencesC = countFasta(options.outputfile) if int(readsC) == 0 and int(sequencesC) == 0: print readsC, sequencesC raise Exception rcType = ReadCountType(Name='qualityFiltered', insertIfNeeded=True) ReadCount(Sequence_File_ID=options.Sequence_File_ID, Reads=readsC, Sequences=sequencesC, Read_Count_Type_ID=rcType, insertIfNeeded=True)
def main(args): parser = OptionParser('usage: %prog [options]') optionsAvailable = ( ('-i', '--input', 'inputfile', 'string'), ('-f', '--filterid', 'Blast_Filter_Protocol_ID', 'int'), ('-s', '--sequencefileid', 'Sequence_File_ID', 'int'), ) for oa in optionsAvailable: parser.add_option(oa[0], oa[1], dest=oa[2], type=oa[3]) (options, args) = parser.parse_args(args) outputs = applyFilterProtocol(options.inputfile, options.Blast_Filter_Protocol_ID) protocol = BlastFilterProtocol(options.Blast_Filter_Protocol_ID) stepsC = len(list(protocol.steps())) for fn in outputs: parts = fn.split('.')[-(stepsC+1):][:-1] rcType = ReadCountType(Name=''.join(parts), insertIfNeeded=True) readsC, sequencesC = countFasta(fn) if readsC == 0 and sequencesC == 0: raise Exception ReadCount(Sequence_File_ID=options.Sequence_File_ID, Reads=readsC, Sequences=sequencesC, Read_Count_Type_ID=rcType, insertIfNeeded=True)
def main(args): parser = OptionParser('usage: %prog [options]') optionsAvailable = ( ('-i', '--input', 'inputfile', 'string'), ('-o', '--output', 'outputfile', 'string'), ('-s', '--sequencefileid', 'Sequence_File_ID', 'int'), ) for oa in optionsAvailable: parser.add_option(oa[0], oa[1], dest=oa[2], type=oa[3]) (options, args) = parser.parse_args(args) runCommand((FASTA_FILTER_PATH, '-Q', '-d', options.inputfile)) output = '.'.join((os.path.splitext(options.inputfile)[0], 'noDups', 'fastq')) readsC, sequencesC = countFasta(options.outputfile) if readsC == 0 and sequencesC == 0: raise Exception rcType = ReadCountType(Name='noDups', insertIfNeeded=True) ReadCount(Sequence_File_ID=options.Sequence_File_ID, Reads=readsC, Sequences=sequencesC, Read_Count_Type_ID=rcType, insertIfNeeded=True)