def trim(source_left, source_right, dest_left, dest_right):
fastq_pairs = itertools.izip(
FastqStanza.stanza_generator(source_left), FastqStanza.stanza_generator(source_right))
for (left_stanza, right_stanza) in fastq_pairs:
FastqStanza.trim_to_shortest_sequence_length(left_stanza, right_stanza)
dest_left.write(left_stanza.as_text())
dest_right.write(right_stanza.as_text())
def demultiplex(left_fastq, right_fastq, barcode_files):
fastq_pairs = itertools.izip(FastqStanza.stanza_generator(left_fastq),
FastqStanza.stanza_generator(right_fastq))
for (left_stanza, right_stanza) in fastq_pairs:
assert_sequence_ids_match(left_stanza, right_stanza)
barcode = left_stanza.sequence_id.split(':')[0][1:]
try:
(left_out, right_out) = barcode_files[barcode]
except KeyError:
raise UndefinedBarcodeError(left_stanza)
left_out.write(left_stanza.as_text())
right_out.write(right_stanza.as_text())
def demultiplex(left_fastq, right_fastq, barcode_files):
fastq_pairs = itertools.izip(
FastqStanza.stanza_generator(left_fastq), FastqStanza.stanza_generator(right_fastq))
for (left_stanza, right_stanza) in fastq_pairs:
assert_sequence_ids_match(left_stanza, right_stanza)
barcode = left_stanza.sequence_id.split(':')[0][1:]
try:
(left_out, right_out) = barcode_files[barcode]
except KeyError:
raise UndefinedBarcodeError(left_stanza)
left_out.write(left_stanza.as_text())
right_out.write(right_stanza.as_text())