def test_barcode_matches_no_match():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with a
non-matching record.
"""
record = "@X1:Tag_AAA_ 1:N:0:XXXXXXXX"
barcode = "AAC"
assert not barcodes_umis.barcode_matches(record, barcode)
def test_barcode_matches_two_mismatch():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with 2
allowed mismatches and a non-matching record.
"""
record = "@X1:Tag_ACC_ 1:N:0:XXXXXXXX"
barcode = "AAA"
assert barcodes_umis.barcode_matches(record, barcode, 2)
def test_barcode_matches():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with default
mismatches and delimiter.
"""
record = "@X1:Tag_AAA_ 1:N:0:XXXXXXXX"
barcode = "AAA"
assert barcodes_umis.barcode_matches(record, barcode)
def test_barcode_matches_one_mismatch_false():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with 1
allowed mismatch and a non-matching record.
"""
record = "@X1:Tag_ACC_ 1:N:0:XXXXXXXX"
barcode = "AAA"
assert not barcodes_umis.barcode_matches(record, barcode, 1)
def test_barcode_matches_one_mismatch():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with 1
allowed mismatch.
"""
record = "@X1:Tag_AAC_ 1:N:0:XXXXXXXX"
barcode = "AAA"
assert barcodes_umis.barcode_matches(record, barcode, 1)
def test_barcode_matches_no_barcode():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with a
record with no barcode.
"""
record = "@X1:Tag 1:N:0:XXXXXXXX"
barcode = "AAA"
assert not barcodes_umis.barcode_matches(record, barcode)
def test_barcode_matches_delimiter():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with a
non-default delimiter.
"""
record = "@X1:Tag.AAA. 1:N:0:XXXXXXXX"
barcode = "AAA"
assert barcodes_umis.barcode_matches(record, barcode, delimiter=".")
def test_barcode_matches_different_length_barcode():
"""
Test :py:func:`riboviz.barcodes_umis.barcode_matches` with a
record with that has a barcode a different length from that being
matched.
"""
record = "@X1:Tag_AAAA_ 1:N:0:XXXXXXXX"
barcode = "AAA"
assert not barcodes_umis.barcode_matches(record, barcode)
def assign_sample(fastq_record1, fastq_record2, barcode, read1_split_fh,
read2_split_fh, is_paired_end, mismatches, delimiter):
"""
Check if a FASTQ record matches a barcode for a sample and, if so,
add the record to the FASTQ output file for that sample.
:param fastq_record1: FASTQ record
:type fastq_record1: list(str or unicode)
:param fastq_record2: FASTQ record for paired read, or ``None``
:type fastq_record2: list(str or unicode)
:param barcode: Barcode
:type barcode: str or unicode
:param read1_split_fh: Read 1 output file handle
:type read1_split_fh: io.IOBase
:param read2_split_fh: Read 2 output file handle, or ``None``
:type read2_split_fh: io.IOBase
:param is_paired_end: Are paired reads being used? (if \
``True`` then ``fastq_record2`` is assumed to have a FASTQ \
record and ``read2_split_fh`` is assumed to be an output \
file handle, not ``None``)
:type is_paired_end: bool
:param mismatches: Mismatches allowed
:type mismatches: int
:param delimiter: Barcode delimiter
:type delimiter: str or unicode
:returns: `True` if FASTQ record matches barcode
:rtype: bool
"""
is_assigned = False
if barcodes_umis.barcode_matches(fastq_record1[0], barcode, mismatches,
delimiter):
is_assigned = True
read1_split_fh.writelines(fastq_record1)
if is_paired_end:
read2_split_fh.writelines(fastq_record2)
return is_assigned