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#!/usr/bin/env python
"""Unit tests for GFF and related parsers.
"""
import os
from io import StringIO
from pathlib import Path
from unittest import TestCase, main
from cogent3.parse.gff import *
__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Matthew Wakefield"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Matthew Wakefield"
__email__ = "wakefield@wehi.edu.au"
__status__ = "Production"
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)
if __name__ == "__main__":
main()
|
