def merge_amplicons(sequence_5p, sequence_3p, output):
file_list = [sequence_5p, sequence_3p]
filetype = consensus_filetype(file_list)
alignment_file = align_amplicons(filetype, sequence_5p, sequence_3p)
positions = parse_alignment_positions(alignment_file)
sequences = read_sequences(filetype, file_list)
merged = merge_sequences(filetype, sequences, positions)
write_sequences(filetype, merged, output)
def merge_amplicons( sequence_5p, sequence_3p, output ):
file_list = [sequence_5p, sequence_3p]
filetype = consensus_filetype( file_list )
alignment_file = align_amplicons( filetype, sequence_5p, sequence_3p )
positions = parse_alignment_positions( alignment_file )
sequences = read_sequences( filetype, file_list )
merged = merge_sequences( filetype, sequences, positions )
write_sequences( filetype, merged, output )
def merge_amplicons(sequence_5p, sequence_3p, reference, output):
file_list = [sequence_5p, sequence_3p]
filetype = consensus_filetype(file_list)
sequences = read_sequences(filetype, file_list)
alignment_left = align_amplicons(sequence_5p, reference)
alignment_right = align_amplicons(sequence_3p, reference)
positions_left = parse_alignment_positions(alignment_left)
positions_right = parse_alignment_positions(alignment_right)
pairs = pair_sequences(positions_left, positions_right)
check_overlap(pairs)
merged = merge_sequences(filetype, sequences, pairs)
write_sequences(filetype, merged, output)
def merge_amplicons(sequence_5p, sequence_3p, reference, output):
file_list = [sequence_5p, sequence_3p]
filetype = consensus_filetype(file_list)
sequences = read_sequences(filetype, file_list)
alignment_left = align_amplicons(sequence_5p, reference)
alignment_right = align_amplicons(sequence_3p, reference)
positions_left = parse_alignment_positions(alignment_left)
positions_right = parse_alignment_positions(alignment_right)
pairs = pair_sequences(positions_left, positions_right)
check_overlap(pairs)
merged = merge_sequences(filetype, sequences, pairs)
write_sequences(filetype, merged, output)
