예제 #1
0
        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':
예제 #2
0
    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(
            {
예제 #3
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    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,
예제 #4
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                         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,