BOWTIE2: ' -x %(reference_genome)s -f -U %(input_file)s -S %(output_file)s', SOAP: ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file)s' }[options.aligner] logm('Aligner command: %s' % aligner_command) # single end reads if options.rrbs: # RRBS scan bs_rrbs(options.infilename, options.rrbs_taginfo, options.adapter_file, options.cutnumber1, options.cutnumber2, options.no_split, indexname, aligner_command, db_path, tmp_path, outfile, XS_pct, XS_count) else: # Normal single end scan bs_single_end(options.infilename, asktag, options.adapter_file, options.cutnumber1, options.cutnumber2, options.no_split, indexname, aligner_command, db_path, tmp_path, outfile, XS_pct, XS_count) else: logm('Pair end') # pair end specific default options aligner_options = dict({ BOWTIE: { '--ff': asktag == 'N', '--fr': asktag == 'Y', '-X': options.max_insert_size, '-I': options.min_insert_size if options.min_insert_size > 0 else None
RMAP : ' -c %(reference_genome)s.fa -o %(output_file)s %(input_file)s' }[options.aligner] logm('Aligner command: %s' % aligner_command) # single end reads if options.rrbs: # RRBS scan bs_rrbs(options.infilename, 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, options.cut_format) else: # Normal single end scan bs_single_end(options.infilename, 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) else: logm('Pair end') # pair end specific default options aligner_options = dict( { BOWTIE: { '--fr': True, '-X': options.max_insert_size, '-I': options.min_insert_size
options.adapter_file, options.cutnumber1, options.cutnumber2, options.no_split, indexname, aligner_command, db_path, tmp_path, outfile) else: # Normal single end scan bs_single_end( options.infilename, asktag, options.adapter_file, options.cutnumber1, options.cutnumber2, options.no_split, indexname, aligner_command, db_path, tmp_path, outfile ) else: logm('Pair end') # pair end specific default options aligner_options = dict({BOWTIE: {'--ff' : asktag == 'N', '--fr' : asktag == 'Y', '-X' : options.max_insert_size, '-I' : options.min_insert_size if options.min_insert_size > 0 else None }, BOWTIE2 : { '--ff' : asktag == 'N',
XS_count, options.adapter_mismatch, options.Output_multiple_hit, options.Output_unmapped_hit, options.cut_format ) else: # Normal single end scan bs_single_end( options.infilename, 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 ) else: logm('Pair end') # pair end specific default options aligner_options = dict({BOWTIE: {'--fr' : True, '-X' : options.max_insert_size, '-I' : options.min_insert_size if options.min_insert_size > 0 else None, '-a' : True # "-k 2" in bowtie would not report the best two