logm('Single end') aligner_command = aligner_exec + aligner_options_string() + { BOWTIE: ' %(reference_genome)s -f %(input_file)s %(output_file)s', 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':
logm('Reduced Representation Bisulfite Sequencing: %s' % str(options.rrbs)) if options.infilename is not None: logm('Single end') aligner_command = aligner_exec + aligner_options_string() + \ { BOWTIE : ' -k 2 %(reference_genome)s -f %(input_file)s %(output_file)s', BOWTIE2 : ' -k 2 -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', 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( {
logm('Reduced Representation Bisulfite Sequencing: %s' % str(options.rrbs)) if options.infilename is not None: logm('Single end') aligner_command = aligner_exec + aligner_options_string() + { BOWTIE : ' %(reference_genome)s -f %(input_file)s %(output_file)s', 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) 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,
BOWTIE2 : ' -k 2 -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', 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, 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, 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,