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src/q/i/qiime-1.8.0/qiime/extract_barcodes.py   qiime(Download)
    bc_qual = read1_data[quality_index][:bc1_len]
    if rev_comp_bc1:
        bc_read = DNA.rc(bc_read)
        bc_qual = bc_qual[::-1]
 
    bc_qual2 = read2[quality_index][0:bc2_len]
    if rev_comp_bc1:
        bc_read1 = DNA.rc(bc_read1)
        bc_qual1 = bc_qual1[::-1]
    if rev_comp_bc2:
        bc_read2 = DNA.rc(bc_read2)
            for curr_primer in reverse_primers:
                if curr_primer.search(read_data[sequence_index]):
                    read_seq = DNA.rc(read_seq)
                    read_qual = read_qual[::-1]
                    found_primer_match = True
 
    if rev_comp_bc1:
        bc_read1 = DNA.rc(bc_read1)
        bc_qual1 = bc_qual1[::-1]
    if rev_comp_bc2:

src/q/i/qiime-1.8.0/qiime/pycogent_backports/uclust.py   qiime(Download)
        if target_rev_match:
            query_id = uc_query_id + ' RC'
            aligned_query = DNA.rc(aligned_query)
            target_id = uc_target_id
            aligned_target = DNA.rc(aligned_target)

src/p/y/pynast-1.2.2/pynast/pycogent_backports/uclust.py   pynast(Download)
        if target_rev_match:
            query_id = uc_query_id + ' RC'
            aligned_query = DNA.rc(aligned_query)
            target_id = uc_target_id
            aligned_target = DNA.rc(aligned_target)

src/c/o/cogent-1.5.3/cogent/app/uclust.py   cogent(Download)
        if target_rev_match:
            query_id = uc_query_id + ' RC'
            aligned_query = DNA.rc(aligned_query)
            target_id = uc_target_id
            aligned_target = DNA.rc(aligned_target)

src/p/y/pycogent-HEAD/cogent/app/uclust.py   pycogent(Download)
        if target_rev_match:
            query_id = uc_query_id + ' RC'
            aligned_query = DNA.rc(aligned_query)
            target_id = uc_target_id
            aligned_target = DNA.rc(aligned_target)

src/q/i/qiime-1.8.0/qiime/split_libraries_fastq.py   qiime(Download)
            barcode = bc_data[sequence_index]
        if rev_comp_barcode:
            barcode = DNA.rc(barcode)
        # Grab the read sequence
        sequence = read_data[1]
 
        if rev_comp:
            sequence = DNA.rc(sequence)
            quality = quality[::-1]
 

src/q/i/qiime-1.8.0/scripts/split_libraries_fastq.py   qiime(Download)
 
        if rev_comp_mapping_barcodes:
            barcode_to_sample_id = {DNA.rc(k):v for k, v in
                barcode_to_sample_id.iteritems()}
 

src/q/i/qiime-1.8.0/qiime/util.py   qiime(Download)
    revcomp_barcode_mapping_column=[]
    for i in barcode_mapping_column:
        revcomp_barcode_mapping_column.append(DNA.rc(i))
        barcode_len=len(i)
    revcomp_barcode_mapping_column=set(revcomp_barcode_mapping_column)

src/q/i/qiime-1.8.0/qiime/truncate_reverse_primer.py   qiime(Download)
        try:
            reverse_primers[curr_id] =\
             [DNA.rc(curr_rev_primer) for curr_rev_primer in\
             id_map[curr_id]['ReversePrimer'].split(',')]
        except KeyError:

src/q/i/qiime-1.8.0/qiime/split_libraries.py   qiime(Download)
        # proper orientation with the input fasta sequences
        rev_primers[n[1]['BarcodeSequence']]=\
         [DNA.rc(curr_rev_primer) for curr_rev_primer in\
         (n[1]['ReversePrimer']).split(',')]
 

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