1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
|
import numpy as np
from gtfparse import (
parse_gtf,
parse_gtf_and_expand_attributes,
REQUIRED_COLUMNS,
ParsingError
)
from six import StringIO
from pytest import raises as assert_raises
gtf_text = """
# sample GTF data copied from:
# http://useast.ensembl.org/info/website/upload/gff.html?redirect=no
1\ttranscribed_unprocessed_pseudogene\tgene\t11869\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
1\tprocessed_transcript\ttranscript\t11869\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana";
"""
def test_parse_gtf_lines_with_expand_attributes():
parsed_dict = parse_gtf_and_expand_attributes(StringIO(gtf_text))
# excluding 'attribute' column from required names
expected_columns = REQUIRED_COLUMNS[:8] + [
"gene_id",
"gene_name",
"gene_source",
"gene_biotype",
"transcript_id",
"transcript_name",
"transcript_source",
]
# convert to list since Py3's dictionary keys are a distinct collection type
assert list(parsed_dict.keys()) == expected_columns
assert list(parsed_dict["seqname"]) == ["1", "1"]
# convert to list for comparison since numerical columns may be NumPy arrays
assert list(parsed_dict["start"]) == [11869, 11869]
assert list(parsed_dict["end"]) == [14409, 14409]
# can't compare NaN with equality
scores = list(parsed_dict["score"])
assert np.isnan(scores).all(), "Unexpected scores: %s" % scores
assert list(parsed_dict["gene_id"]) == ["ENSG00000223972", "ENSG00000223972"]
assert list(parsed_dict["transcript_id"]) == ["", "ENST00000456328"]
def test_parse_gtf_lines_without_expand_attributes():
parsed_dict = parse_gtf(StringIO(gtf_text))
# convert to list since Py3's dictionary keys are a distinct collection type
assert list(parsed_dict.keys()) == REQUIRED_COLUMNS
assert list(parsed_dict["seqname"]) == ["1", "1"]
# convert to list for comparison since numerical columns may be NumPy arrays
assert list(parsed_dict["start"]) == [11869, 11869]
assert list(parsed_dict["end"]) == [14409, 14409]
# can't compare NaN with equality
scores = list(parsed_dict["score"])
assert np.isnan(scores).all(), "Unexpected scores: %s" % scores
assert len(parsed_dict["attribute"]) == 2
def test_parse_gtf_lines_error_too_many_fields():
bad_gtf_text = gtf_text.replace(" ", "\t")
# pylint: disable=no-value-for-parameter
with assert_raises(ParsingError):
parse_gtf(StringIO(bad_gtf_text))
def test_parse_gtf_lines_error_too_few_fields():
bad_gtf_text = gtf_text.replace("\t", " ")
# pylint: disable=no-value-for-parameter
with assert_raises(ParsingError):
parse_gtf(StringIO(bad_gtf_text))
|
