if options.min_insert_size > 0 else None, '--no-discordant': True, '--no-mixed': True }, SOAP: { '-x': options.max_insert_size, '-m': options.min_insert_size if options.min_insert_size > 0 else 100 } }[options.aligner], **aligner_options) aligner_command = aligner_exec + aligner_options_string() + { BOWTIE: ' %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s %(output_file)s', BOWTIE2: ' -x %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s -S %(output_file)s', SOAP: ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file_1)s -b %(input_file_2)s -2 %(output_file)s.unpaired' }[options.aligner] logm('Aligner command: %s' % aligner_command) bs_pair_end(options.infilename_1, options.infilename_2, asktag, options.adapter_file, options.cutnumber1, options.cutnumber2, options.no_split, indexname, aligner_command, db_path, tmp_path, outfile, XS_pct, XS_count) outfile.close()
aligner_command = aligner_exec + aligner_options_string() + \ { BOWTIE : ' %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s %(output_file)s', BOWTIE2 : ' -x %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s -S %(output_file)s', SOAP : ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file_1)s -b %(input_file_2)s -2 %(output_file)s.unpaired' #, # RMAP : # rmappe, also paste two inputs into one file. }[options.aligner] logm('Aligner command: %s' % aligner_command) if '--end-to-end' not in aligner_options: aligner_options_defaults[BOWTIE2].update({'-D': 50}) else: aligner_options_defaults[BOWTIE2].update({ '-D': 50, '-L': 15, '--score-min': 'L,-0.6,-0.6' }) bs_pair_end(options.infilename_1, options.infilename_2, asktag, options.adapter_file, options.cutnumber1, options.cutnumber2, options.no_split, str_no_mismatches, aligner_command, db_path, tmp_path, outfile, XS_pct, XS_count, options.adapter_mismatch, options.Output_multiple_hit, options.Output_unmapped_hit) outfile.close()
'--no-mixed' : True }, SOAP: { '-x' : options.max_insert_size, '-m' : options.min_insert_size if options.min_insert_size > 0 else 100 }}[options.aligner], **aligner_options) aligner_command = aligner_exec + aligner_options_string() + { BOWTIE : ' %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s %(output_file)s', BOWTIE2 : ' -x %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s -S %(output_file)s', SOAP : ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file_1)s -b %(input_file_2)s -2 %(output_file)s.unpaired'}[options.aligner] logm('Aligner command: %s' % aligner_command) bs_pair_end(options.infilename_1, options.infilename_2, asktag, options.adapter_file, options.cutnumber1, options.cutnumber2, options.no_split, indexname, aligner_command, db_path, tmp_path, outfile ) outfile.close()
}[options.aligner] logm('Aligner command: %s' % aligner_command) if '--end-to-end' not in aligner_options: aligner_options_defaults[BOWTIE2].update({'-D' : 50}) else: aligner_options_defaults[BOWTIE2].update({'-D' : 50, '-L': 15, '--score-min': 'L,-0.6,-0.6' }) bs_pair_end(options.infilename_1, options.infilename_2, asktag, options.adapter_file, int(options.cutnumber1), int(options.cutnumber2), options.no_split, str_no_mismatches, aligner_command, db_path, tmp_path, outfile, XS_pct, XS_count, options.adapter_mismatch, options.Output_multiple_hit, options.Output_unmapped_hit ) outfile.close()