def test_slideseq2(self):
bam_fp = pipeline.convert_fastqs_to_unmapped_bam(
self.fastq_slideseq2_fps,
"slideseq2",
tempfile.mkdtemp(),
name="test",
)
with pysam.AlignmentFile(bam_fp, "rb", check_sq=False) as f:
alignments = list(f.fetch(until_eof=True))
self.assertEqual(2, len(alignments))
self.assertEqual(
[
"NB501583:801:H7JLTBGXH:1:11101:20912:1050",
"NB501583:801:H7JLTBGXH:1:11101:8670:1050",
],
[al.query_name for al in alignments],
)
self.assertEqual(
[
read.sequence
for read in ngs.fastq.Fastq(self.fastq_slideseq2_fps[1])
],
[al.query_sequence for al in alignments],
)
self.assertEqual(
[
read.qualities.string
for read in ngs.fastq.Fastq(self.fastq_slideseq2_fps[1])
],
[
pysam.array_to_qualitystring(al.query_qualities)
for al in alignments
],
)
self.assertEqual(
{
("UR", "TTTTTTTTT"),
("UY", "EEEEEEEEE"),
("CR", "CTTTGNTCAATGTT"),
("CY", "AAAAA#EEAEEEEE"),
("RG", "test"),
},
set(alignments[0].get_tags()),
)
self.assertEqual(
{
("UR", "AGTGTCTCA"),
("UY", "EAEAEAEEE"),
("CR", "CTCTTNATCCTCAT"),
("CY", "AAAAA#EEE/EAE/"),
("RG", "test"),
},
set(alignments[1].get_tags()),
)
def test_indropsv3(self):
bam_fp = pipeline.convert_fastqs_to_unmapped_bam(
self.fastq_indropsv3_fps,
"indropsv3",
tempfile.mkdtemp(),
name="test",
)
with pysam.AlignmentFile(bam_fp, "rb", check_sq=False) as f:
alignments = list(f.fetch(until_eof=True))
self.assertEqual(2, len(alignments))
self.assertEqual(
[
"M03718:773:000000000-JKHP3:1:1101:18272:1693",
"M03718:773:000000000-JKHP3:1:1101:17963:1710",
],
[al.query_name for al in alignments],
)
self.assertEqual(
[
read.sequence
for read in ngs.fastq.Fastq(self.fastq_10xv3_fps[1])
],
[al.query_sequence for al in alignments],
)
self.assertEqual(
[
read.qualities.string
for read in ngs.fastq.Fastq(self.fastq_10xv3_fps[1])
],
[
pysam.array_to_qualitystring(al.query_qualities)
for al in alignments
],
)
self.assertEqual(
{
("UR", "CCAAAA"),
("UY", "FFBFGG"),
("CR", "TACGTCATCTCCTACG"),
("CY", "1111AFAF1111AFAF"),
("RG", "test"),
},
set(alignments[0].get_tags()),
)
self.assertEqual(
{
("UR", "TTAGAA"),
("UY", "FAAAFF"),
("CR", "TTAGATCGTTAGATCG"),
("CY", "1>>11DFA1>>11DFA"),
("RG", "test"),
},
set(alignments[1].get_tags()),
)