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"""Unit tests for GFF and related parsers.
"""
import os
import re
from io import StringIO
from pathlib import Path
from unittest import TestCase
import pytest
from cogent3.parse.gff import gff_parser, parse_attributes_gff2
headers = [
"""##gff-version 2
##source-version <source> <version text>
##date <date>
##Type <type> [<seqname>]
##DNA <seqname>
##acggctcggattggcgctggatgatagatcagacgac
##...
##end-DNA
""",
"""##gff-version 2
""",
"",
]
# '<seqname>\t<source>\t<feature>\t<start>\t<end>\t<score>\t<strand>\t<frame>\t[attribute]\n'
data_lines = [
(
'seq1\tBLASTX\tsimilarity\t101\t235\t87.1\t+\t0\tTarget "HBA_HUMAN" 11 55 ; E_value 0.0003\n',
(
"seq1",
"BLASTX",
"similarity",
100,
235,
"87.1",
"+",
"0",
'Target "HBA_HUMAN" 11 55 ; E_value 0.0003',
None,
),
),
(
'dJ102G20\tGD_mRNA\tcoding_exon\t7105\t7201\t.\t-\t2\tSequence "dJ102G20.C1.1"\n',
(
"dJ102G20",
"GD_mRNA",
"coding_exon",
7201,
7104,
".",
"-",
"2",
'Sequence "dJ102G20.C1.1"',
None,
),
),
(
"dJ102G20\tGD_mRNA\tcoding_exon\t7105\t7201\t.\t-\t2\t\n",
("dJ102G20", "GD_mRNA", "coding_exon", 7201, 7104, ".", "-", "2", "", None),
),
(
'12345\tSource with spaces\tfeature with spaces\t-100\t3600000000\t1e-5\t-\t.\tSequence "BROADO5" ; Note "This is a \\t tab containing \\n multi line comment"\n',
(
"12345",
"Source with spaces",
"feature with spaces",
3600000000,
101,
"1e-5",
"-",
".",
'Sequence "BROADO5" ; Note "This is a \\t tab containing \\n multi line comment"',
None,
),
),
]
class GffTest(TestCase):
"""Setup data for all the GFF parsers."""
def testGffParserData(self):
"""Test gff_parser with valid data lines"""
for line, canned_result in data_lines:
result = next(gff_parser(StringIO(line)))
canned_result = list(canned_result)
self.assertEqual(result.pop("Attributes")["Info"], canned_result.pop(8))
self.assertEqual(set(result.values()), set(canned_result))
def test_gff_parser_headers(self):
"""Test gff_parser with valid data headers"""
data = "".join([x[0] for x in data_lines])
for header in headers:
result = list(gff_parser(StringIO(header + data)))
lines = [(x[0], list(x[1])) for x in data_lines]
self.assertEqual(
[l.pop("Attributes")["Info"] for l in result],
[x[1].pop(8) for x in lines],
)
self.assertEqual(
[set(l.values()) for l in result], [set(x[1]) for x in lines]
)
def test_parse_attributes_gff2(self):
"""Test the parse_attributes_gff2 method"""
self.assertEqual(
[
parse_attributes_gff2(x[1][8], (x[1][3], x[1][4]))["ID"]
for x in data_lines
],
["HBA_HUMAN", "dJ102G20.C1.1", "", "BROADO5"],
)
def test_gff2_parser_string(self):
"""Test the gff_parser works with a string filepath"""
filepath = os.path.join("data/gff2_test.gff")
for i, result in enumerate(gff_parser(filepath)):
line = list(data_lines[i][1])
self.assertEqual(result.pop("Attributes")["Info"], line.pop(8))
self.assertEqual(set(result.values()), set(line))
def test_gff2_parser_path(self):
"""Test the gff_parser works with a pathlib.Path filepath"""
filepath = Path("data/gff2_test.gff")
for i, result in enumerate(gff_parser(filepath)):
line = list(data_lines[i][1])
self.assertEqual(result.pop("Attributes")["Info"], line.pop(8))
self.assertEqual(set(result.values()), set(line))
def test_gff3_parser(self):
"""Test the gff_parser works on a gff3 file"""
gff3_path = os.path.join("data/c_elegans_WS199_shortened_gff.gff3")
for i, result in enumerate(gff_parser(gff3_path)):
self.assertEqual(len(result), 10)
# 15 total lines, but 2 comments
self.assertEqual(i + 1, 15 - 2)
def test_custom_attr_func(self):
"""user provided attr parser"""
gff3_path = os.path.join("data/c_elegans_WS199_shortened_gff.gff3")
for result in gff_parser(gff3_path, attribute_parser=lambda x, y: x):
self.assertIsInstance(result["Attributes"], str)
@pytest.fixture
def multi_seqid_path(DATA_DIR, tmp_path):
gff_path = DATA_DIR / "ensembl_sample.gff3"
data = gff_path.read_text().splitlines()
# add two new seqid's using the last 4 lines, twice
change = data[-4:]
data.extend(_modify_lines(change, "3"))
data.extend(_modify_lines(change, "4"))
outpath = tmp_path / "ensembl-edited.gff3"
outpath.write_text("\n".join(data))
return outpath
def _modify_lines(change, seqid: str) -> list:
ident = re.compile(r"ENS[GT]\d+")
result = []
for line in change:
# change all identifiers so each seqid has unique identifiers
for match in ident.findall(line):
line = line.replace(match, f"{match}{seqid}")
line = line.split("\t")
line[0] = seqid
line = "\t".join(line)
result.append(line)
return result
@pytest.mark.parametrize("seqids", ("22", ("3",), ("3", "4")))
def test_seq_names(multi_seqid_path, seqids):
got = {r["SeqID"] for r in gff_parser(multi_seqid_path, seqids=seqids)}
expect = {seqids} if isinstance(seqids, str) else set(seqids)
assert got == expect
def test_no_seq_names(multi_seqid_path):
got = {r["SeqID"] for r in gff_parser(multi_seqid_path, seqids=None)}
expect = {"22", "3", "4"}
assert got == expect
def test_parse_field_spaces(DATA_DIR):
path = DATA_DIR / "simple.gff"
got = list(gff_parser(path))
for record in got:
for value in record.values():
if isinstance(value, str):
assert value.strip() == value, "should not have spaces!"
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