def test_no_required_attributes(self):
"""
Raise error if transcript_id attribute is not present.
"""
gtf = make_file_from_list([
['1', '.', 'transcript', '500', '600', '.', '+', '.', 'gene_id "G1";'],
])
message = "First element in gene content is neither gene or transcript!"
with self.assertRaisesRegex(Exception, message):
list((segment._get_gene_content(gtf, ['1', 'MT'])))
def test_all_good(self):
"""
* second gene has no 'gene' interval - but it is present in output as it should
* last interval is on chromosome 2, but it is not in the output
"""
gtf_data = list_to_intervals([
['1', '.', 'gene', '100', '300', '.', '+', '.',
'gene_id "G1";'],
['1', '.', 'transcript', '100', '250', '.', '+', '.',
'gene_id "G1"; transcript_id "T1";'],
['1', '.', 'exon', '100', '150', '.', '+', '.',
'gene_id "G1"; transcript_id "T1"; exon_number "1";'],
['1', '.', 'exon', '200', '250', '.', '+', '.',
'gene_id "G1"; transcript_id "T1"; exon_number "2";'],
['1', '.', 'transcript', '150', '300', '.', '+', '.',
'gene_id "G1"; transcript_id "T2";'],
['1', '.', 'exon', '150', '200', '.', '+', '.',
'gene_id "G1"; transcript_id "T2"; exon_number "1";'],
['1', '.', 'exon', '250', '300', '.', '+', '.',
'gene_id "G1"; transcript_id "T2"; exon_number "2";'],
['1', '.', 'transcript', '400', '500', '.', '+', '.',
'gene_id "G2"; transcript_id "T3";'],
['1', '.', 'exon', '400', '430', '.', '+', '.',
'gene_id "G2"; transcript_id "T3"; exon_number "1"'],
['1', '.', 'CDS', '410', '430', '.', '+', '.',
'gene_id "G2"; transcript_id "T3";'],
['1', '.', 'exon', '470', '500', '.', '+', '.',
'gene_id "G2"; transcript_id "T3"; exon_number "2"'],
['1', '.', 'CDS', '470', '490', '.', '+', '.',
'gene_id "G2"; transcript_id "T3";'],
['2', '.', 'CDS', '470', '490', '.', '+', '.',
'gene_id "G3"; transcript_id "T4";'],
])
gtf = make_file_from_list(intervals_to_list(gtf_data))
gene1, gene2 = list(segment._get_gene_content(gtf, ['1', 'MT'], report_progress=True))
expected1 = {
'gene': gtf_data[0],
'T1': gtf_data[1:4],
'T2': gtf_data[4:7],
}
extra_gene = create_interval_from_list(
['1', '.', 'gene', '400', '500', '.', '+', '.', 'gene_id "G2";'])
expected2 = {
'gene': extra_gene,
'T3': gtf_data[7:-1],
}
self.assertEqual(gene1, expected1)
self.assertEqual(gene2, expected2)
def test_already_processed_gene(self):
"""
Raise error if member of already processed gene is found.
"""
gtf = make_file_from_list([
['1', '.', 'gene', '100', '300', '.', '+', '.', 'gene_id "G1";'],
['1', '.', 'transcript', '100', '250', '.', '+', '.', 'gene_id "G1"; transcript_id "T1";'],
['1', '.', 'gene', '500', '700', '.', '+', '.', 'gene_id "G2";'],
['1', '.', 'transcript', '500', '600', '.', '+', '.', 'gene_id "G1"; transcript_id "T3";'],
])
with self.assertRaises(AssertionError):
list((segment._get_gene_content(gtf, ['1', 'MT'])))
def test_already_processed(self):
"""
Raise error if member of already processed transcript is found.
"""
gtf = make_file_from_list([
['1', '.', 'gene', '100', '300', '.', '+', '.', 'gene_id "G1";'],
['1', '.', 'transcript', '100', '250', '.', '+', '.', 'gene_id "G1"; transcript_id "T1";'],
['1', '.', 'transcript', '150', '300', '.', '+', '.', 'gene_id "G1"; transcript_id "T2";'],
['1', '.', 'exon', '150', '200', '.', '+', '.', 'gene_id "G1"; transcript_id "T1"; exon_number "1";'],
])
with self.assertRaises(AssertionError):
next((segment._get_gene_content(gtf, ['1', 'MT'])))