def test_no_fa_exception(self, test_data_dir):
"""INSC1003.gff3 has no sequences"""
gff3_without_fasta = test_data_dir / "INSC1003.gff3"
with pytest.raises(GFF3FastaException):
_ = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(parse_gff3_embedded_fasta(gff3_without_fasta))
)
def test_parse_peg10(self, test_data_dir):
"""PEG10 is a human gene with a -1 frameshift"""
gff3 = test_data_dir / "PEG10_offset_gff3_fasta.gff3"
gff3_rec = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_gff3_embedded_fasta(gff3)))[0]
tx = gff3_rec.genes[0].transcripts[0]
assert not tx.has_in_frame_stop
def test_duplicate_sequence(self, test_data_dir):
fasta = test_data_dir / "INSC1003_extra_contig_duplicate.fa"
gff3 = test_data_dir / "INSC1003.gff3"
gff3_with_fasta = test_data_dir / "INSC1003_embedded_extra_contig_duplicate.gff3"
with pytest.raises(DuplicateSequenceException):
_ = list(parse_gff3_fasta(gff3, fasta))
with pytest.raises(DuplicateSequenceException):
_ = list(parse_gff3_embedded_fasta(gff3_with_fasta))
def test_gff3_with_embedded_fa_extra_contig(self, test_data_dir):
"""Handle FASTA with sequences not seen in the GFF3"""
gff3 = test_data_dir / "INSC1003_embedded_extra_contig.gff3"
recs = list(ParsedAnnotationRecord.parsed_annotation_records_to_model(parse_gff3_embedded_fasta(gff3)))
assert len(recs) == 2
assert recs[1].is_empty
assert recs[0].sequence_name
assert recs[0].sequence
assert recs[1].sequence
assert recs[1].sequence_name == "extraseq"
def test_tbl_export_from_gff3(test_data_dir, tmp_path, gff3, expected_tbl):
gff3 = test_data_dir / gff3
recs = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_gff3_embedded_fasta(gff3)))
tmp = tmp_path / "tmp.tbl"
with open(tmp, "w") as fh:
collection_to_tbl(recs,
fh,
locus_tag_prefix="test",
submitter_lab_name="inscripta",
random_seed=123)
with open(tmp) as fh1, open(test_data_dir / expected_tbl) as fh2:
assert fh1.read() == fh2.read()
def test_parse_inso(self, test_data_dir):
"""This proves we handle frame and phase"""
gbk = test_data_dir / "insO_frameshift.gbk"
gff3 = test_data_dir / "insO_frameshift.gff3"
with open(gbk, "r") as fh:
gbk_rec = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh)))[0]
gff3_rec = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_gff3_embedded_fasta(gff3)))[0]
expected_protein = (
"MKKRNFSAEFKRESAQLVVDQKYTVADAAKAMDVGLSTMTRWVKQLRDERQGKTPKASPITPEQIEIRKLRKKLQRIEMENEILKKNRP"
"EKPDGRRAVLRSQVLELHGISHGSAGARSIATMATRRGYQMGRWLAGRLMKELGLVSCQQPTHRYKRGGHEHVAIPNYLERQFAVTEPNQV"
"WCGDVTYIWTGKRWAYLAVVLDLFARKPVGWAMSFSPDSRLTMKALEMAWETRGKPVGVMFQSDQGSHYTSRQFRQLLWRYRIRQSMSRR"
"GNCWDNSPMERFFRSLKNEWVPATGYVSFSDAAHAITDYIVGYYSALRPHEYNGGLPPNESENRYWKNSNAEASFS*"
)
assert (str(gbk_rec.genes[0].get_primary_protein()) == str(
gff3_rec.genes[0].get_primary_protein()) == expected_protein)