Skip to content

Commit

Permalink
new testdata subset, new test
Browse files Browse the repository at this point in the history
  • Loading branch information
@kedhammar
kedhammar committed Jun 4, 2024
1 parent 4baa2ff commit e71ccee
Showing 1 changed file with 100 additions and 132 deletions.
232 changes: 100 additions & 132 deletions tests/test_anglerfish/test_demux/test_demux.py
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import gzip
import tempfile
from pathlib import Path

Expand All @@ -7,179 +8,146 @@


@pytest.fixture(scope="module")
def tmp_demux_path():
def fixture():
"""Create a temporary directory shared between all tests in this module."""
tmp = tempfile.TemporaryDirectory()
tmp_path = Path(tmp.name)

yield tmp_path
tmp.cleanup()
# Create subset testdata, a single read subset from the testdata
with gzip.open(tmp_path / "testdata.fastq.gz", "wb") as f:
f.write(b"""
@0ad8bdb6-e009-43c5-95b1-d381e699f983 runid=7d98ab9ee7f513f92fd5e382dc3dd563b956e4fa sampleid=Pools read=7283 ch=21 start_time=2020-01-17T15:19:22Z
CGTTGTAGTTCACCAAACCCAACAACCTAGATAGGCCGCACCTAAAATGATACGGCGACCGCGAGATCCCGATTCTGACACTCTTTCCCTACACGACGCTCTTCCGATCTCACAAAATTATTAGGCATGGTGGTGCATGCCTGTGGTCCCAGCTACTTGGGAGGCTGAGGCAGGGAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCCAGACCAGCGCCACTGTACTCCAGCCTGGCAACAAGCAGGAACTCCGTTTCAAAACAAGATCTAGGGTGGTTTTCCCAAGTTAGTCAGGAGATCGGAAGAGCACGTCGGAACTCCAGTCACTAACTTGGTCAACCTAGAAATCTGATGCCGTCTTCTGCTTGTTAGGTGCTGGCCTATCTGGGTGTTGGGTTTGGTTGTATAACGT
+
&&##$$'$()'$$&$&%%%%%%%(*340++1','',,)-*669:98731/0+&&(%&$$$%(',,4$$,&;>@:2$-')&&25<<>/4.,'*$,--**6<;<>)1...2-&%+///+++*%'*1B:<BFDDB=760998EEA?%33115/5-&&3%%/22:+07660*76..7221680('+058)777(@.A?5.-+&'*7)1*-$)))-/1)/'$*%(**.6*),$&&,+%13-2+'%$(%&+&(&'+%$$+.0023<<6946>93;:8618'/&%,%'()344:=:'*6*5$*39090-/4/4)537-/166+)%,'(%'02)5-5@A:/;75&'3?=9=--=;.,/030'9%&&((48977;<=@;3445%'.2<=;51/(.,),*7*%&(,(()&'/01*)'%%$%%(%%$%$
""")

# Create appropriate index file
with open(tmp_path / "truseq.fasta", "w") as f:
f.write(""">truseq_i7
GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG
>truseq_i5
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
""")

fixture = {
"tmp_path": tmp_path,
"testdata": tmp_path / "testdata.fastq.gz",
"index_file": tmp_path / "truseq.fasta",
"paf": tmp_path / "test.paf",
"expected_index": "TAACTTGGTC",
}

yield fixture

tmp.cleanup()

def test_run_minimap2(tmp_demux_path):
paf_path = tmp_demux_path / "test.paf"

def test_run_minimap2(fixture):
to_test.run_minimap2(
fastq_in="testdata/explore/explore_testdata.fastq",
index_file="testdata/explore/illumina_ud.fasta",
output_paf=paf_path,
fastq_in=fixture["testdata"],
index_file=fixture["index_file"],
output_paf=fixture["paf"],
threads=1,
minimap_b=1,
)

# String constructed with explicit whitespaces to avoid issues with tab interpretation
expected = (
"\n".join(
[
"\t".join(
[
"truseq-read_10_C-index_5G",
"130",
"0",
"58",
"+",
"truseq_i5",
"58",
"0",
"58",
"58",
"58",
"60",
"NM:i:0",
"ms:i:348",
"AS:i:348",
"nn:i:0",
"tp:A:P",
"cm:i:16",
"s1:i:54",
"s2:i:0",
"de:f:0",
"rl:i:0",
"cg:Z:58M",
"cs:Z::58",
]
),
"\t".join(
[
"truseq-read_10_C-index_5G",
"130",
"68",
"130",
"+",
"truseq_i7",
"57",
"0",
"57",
"57",
"62",
"60",
"NM:i:5",
"ms:i:333",
"AS:i:328",
"nn:i:0",
"tp:A:P",
"cm:i:15",
"s1:i:54",
"s2:i:0",
"de:f:0.0172",
"rl:i:0",
"cg:Z:33M5I24M",
"cs:Z::33+ggggg:24",
]
),
]
)
+ "\n"
)
expected = "0ad8bdb6-e009-43c5-95b1-d381e699f983\t418\t302\t374\t+\ttruseq_i7\t67\t0\t67\t51\t64\t25\tNM:i:23\tms:i:275\tAS:i:266\tnn:i:10\ttp:A:P\tcm:i:5\ts1:i:29\ts2:i:0\tde:f:0.2388\trl:i:0\tcg:Z:11M2D33M7I21M\tcs:Z::11-ca:6*tg:13*nt*na*na*nc*nt*nt*ng*ng*nt*nc:1*ta:1+ctagaaa:2*gt*tg:17\n0ad8bdb6-e009-43c5-95b1-d381e699f983\t418\t45\t110\t+\ttruseq_i5\t58\t0\t58\t56\t66\t38\tNM:i:10\tms:i:313\tAS:i:305\tnn:i:0\ttp:A:P\tcm:i:10\ts1:i:37\ts2:i:0\tde:f:0.0667\trl:i:0\tcg:Z:15M1D6M7I3M1I33M\tcs:Z::15-a*cg:5+tcccgat:3+g:33\n"
received = open(fixture["paf"]).read()

received = open(paf_path).read()
assert expected == received


def test_parse_paf_lines(tmp_demux_path):
paf_path = tmp_demux_path / "test.paf"

paf_lines_simple = to_test.parse_paf_lines(paf_path)

def test_parse_paf_lines(fixture):
paf_lines_simple = to_test.parse_paf_lines(fixture["paf"])
expected_simple = {
"truseq-read_10_C-index_5G": [
"0ad8bdb6-e009-43c5-95b1-d381e699f983": [
{
"read": "truseq-read_10_C-index_5G",
"adapter": "truseq_i5",
"rlen": 130,
"rstart": 0,
"rend": 58,
"read": "0ad8bdb6-e009-43c5-95b1-d381e699f983",
"adapter": "truseq_i7",
"rlen": 418,
"rstart": 302,
"rend": 374,
"strand": "+",
"cg": "cg:Z:58M",
"cs": "cs:Z::58",
"q": 60,
"cg": "cg:Z:11M2D33M7I21M",
"cs": "cs:Z::11-ca:6*tg:13*nt*na*na*nc*nt*nt*ng*ng*nt*nc:1*ta:1+ctagaaa:2*gt*tg:17",
"q": 25,
"iseq": None,
"sample": None,
},
{
"read": "truseq-read_10_C-index_5G",
"adapter": "truseq_i7",
"rlen": 130,
"rstart": 68,
"rend": 130,
"read": "0ad8bdb6-e009-43c5-95b1-d381e699f983",
"adapter": "truseq_i5",
"rlen": 418,
"rstart": 45,
"rend": 110,
"strand": "+",
"cg": "cg:Z:33M5I24M",
"cs": "cs:Z::33+ggggg:24",
"q": 60,
"cg": "cg:Z:15M1D6M7I3M1I33M",
"cs": "cs:Z::15-a*cg:5+tcccgat:3+g:33",
"q": 38,
"iseq": None,
"sample": None,
},
]
}

assert paf_lines_simple == expected_simple

paf_lines_complex = to_test.parse_paf_lines(paf_path, complex_identifier=True)
paf_lines_complex = to_test.parse_paf_lines(fixture["paf"])
expected_complex = {
"truseq-read_10_C-index_5G_i5_positive": [
"0ad8bdb6-e009-43c5-95b1-d381e699f983": [
{
"read": "truseq-read_10_C-index_5G",
"adapter": "truseq_i5",
"rlen": 130,
"rstart": 0,
"rend": 58,
"read": "0ad8bdb6-e009-43c5-95b1-d381e699f983",
"adapter": "truseq_i7",
"rlen": 418,
"rstart": 302,
"rend": 374,
"strand": "+",
"cg": "cg:Z:58M",
"cs": "cs:Z::58",
"q": 60,
"cg": "cg:Z:11M2D33M7I21M",
"cs": "cs:Z::11-ca:6*tg:13*nt*na*na*nc*nt*nt*ng*ng*nt*nc:1*ta:1+ctagaaa:2*gt*tg:17",
"q": 25,
"iseq": None,
"sample": None,
}
],
"truseq-read_10_C-index_5G_i7_positive": [
},
{
"read": "truseq-read_10_C-index_5G",
"adapter": "truseq_i7",
"rlen": 130,
"rstart": 68,
"rend": 130,
"read": "0ad8bdb6-e009-43c5-95b1-d381e699f983",
"adapter": "truseq_i5",
"rlen": 418,
"rstart": 45,
"rend": 110,
"strand": "+",
"cg": "cg:Z:33M5I24M",
"cs": "cs:Z::33+ggggg:24",
"q": 60,
"cg": "cg:Z:15M1D6M7I3M1I33M",
"cs": "cs:Z::15-a*cg:5+tcccgat:3+g:33",
"q": 38,
"iseq": None,
"sample": None,
}
],
},
]
}

assert paf_lines_complex == expected_complex


def test_parse_cd(tmp_demux_path):
paf_path = tmp_demux_path / "test.paf"
paf_lines_simple = to_test.parse_paf_lines(paf_path)

cs = to_test.parse_cs(
cs_string=paf_lines_simple["truseq-read_10_C-index_5G"][1]["cs"],
index="GGGGG",
umi_before=0,
umi_after=0,
)

#TODO: Finish this test
def test_parse_cd(fixture):
paf_lines_simple = to_test.parse_paf_lines(fixture["paf"])

for read_name, alignments in paf_lines_simple.items():
for alignment in alignments:
cs_string = alignment["cs"]
cs_parsed = to_test.parse_cs(
cs_string=cs_string,
index=fixture["expected_index"],
umi_before=0,
umi_after=0,
)

if alignment["adapter"] == "truseq_i7":
# Perfect match to index
assert cs_parsed[0] == fixture["expected_index"].lower()
assert cs_parsed[1] == 0
elif alignment["adapter"] == "truseq_i5":
# No index, distance the length of all concatenated substitutions of the cs string
assert cs_parsed[0] == ""
assert cs_parsed[1] == 10
else:
raise AssertionError("Case not covered.")

0 comments on commit e71ccee

Please sign in to comment.