def test_sequences(test_data_dir, tmp_path, gbk, flavor):
"""Parse a genbank, write it to disk, then parse it again and compare."""
gbk = test_data_dir / gbk
with open(gbk, "r") as fh:
collections = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh)))
tmp_gbk = tmp_path / "tmp.gbk"
with open(tmp_gbk, "w") as fh:
collection_to_genbank(collections, fh, flavor)
with open(tmp_gbk, "r") as fh:
new_collection = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh)))
assert len(collections[0].genes) == len(new_collection[0].genes)
for gene_a, gene_b in zip(collections[0], new_collection[0]):
assert gene_a._location == gene_b._location
tx_a = gene_a.transcripts[0]
tx_b = gene_b.transcripts[0]
assert tx_a._location == tx_b._location
if tx_a.is_coding:
assert tx_a.cds._location == tx_b.cds._location
assert tx_a.get_protein_sequence() == tx_b.get_protein_sequence()
assert tx_a.get_transcript_sequence() == tx_b.get_transcript_sequence()
def test_missing_translation(test_data_dir, tmp_path):
gbk = test_data_dir / "INSC1003_wrong_missing_translation.gbk"
with open(gbk, "r") as fh:
collections = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh, gbk_type=GenBankParserType.SORTED)))
tmp_gbk = tmp_path / "tmp.gbk"
with open(tmp_gbk, "w") as fh:
collection_to_genbank(collections, fh, update_translations=False)
with open(tmp_gbk, "r") as fh:
annot = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh, gbk_type=GenBankParserType.SORTED)))[0]
genes = annot.genes
assert "translation" not in genes[0].transcripts[0].qualifiers
assert "translation" in genes[1].transcripts[0].qualifiers
assert genes[1].transcripts[0].qualifiers["translation"] == {
"MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWERFCQELGK"
"QIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEE"
"NDIPELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPDTAQRVADWLGKNYLQNQEGF"
"VHICRLDTAGARVLEN"
}
# now export to file and force the translations to be recalculated
tmp_gbk = tmp_path / "tmp.gbk"
with open(tmp_gbk, "w") as fh:
collection_to_genbank(collections, fh, update_translations=True)
with open(tmp_gbk, "r") as fh:
annot = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh, gbk_type=GenBankParserType.SORTED)))[0]
genes = annot.genes
assert genes[0].transcripts[0].qualifiers["translation"] == {
"MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAA"
"QPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLE"
"STVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDAR"
"LLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMK"
"GMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRT"
"LRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWL"
"KNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHV"
"VTPNKKANTSSMDYYHLLRHAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATT"
"LAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVL"
"RYVGNIDEDGACRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV*"
}
assert genes[1].transcripts[0].qualifiers["translation"] == {
"MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWERFCQELGK"
"QIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEE"
"NDIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRE"
"RLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPDTAQRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN*"
}
def test_reserved_attributes(self, test_data_dir, tmp_path):
gb = test_data_dir / "INSC1020_subset_gff3.gb"
parsed = list(parse_genbank(gb))
a = [x.to_annotation_collection() for x in parsed]
tmp_gff = tmp_path / "tmp.gff"
with pytest.warns(ReservedKeyWarning):
with open(tmp_gff, "w") as fh:
collection_to_gff3(a, fh, raise_on_reserved_attributes=False)
with pytest.raises(GFF3ExportException):
with open(tmp_gff, "w") as fh:
collection_to_gff3(a, fh, raise_on_reserved_attributes=True)
def test_broken_frameshift(self, test_data_dir):
"""If I merge the transcript, the frames list no longer matches the location and an exception is raised."""
gbk = test_data_dir / "insO_frameshift.gbk"
with open(gbk, "r") as fh:
gbk_rec = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh)))[0]
cds = gbk_rec.genes[0].get_primary_transcript().cds
cds._location = cds._location.merge_overlapping()
with pytest.raises(MismatchedFrameException):
_ = cds.translate()
def test_records_to_fasta_from_genbank_fasta_header(test_data_dir, tmp_path):
"""Because we are exporting from a ParsedAnnotationRecord directly the FASTA comments are retained."""
gbk = test_data_dir / "INSC1003.gbk"
with open(gbk, "r") as fh:
parsed = parse_genbank(fh)
tmp_fasta = tmp_path / "tmp.fasta"
with open(tmp_fasta, "w") as ofh:
for rec in parsed:
rec.to_fasta(ofh)
with open(tmp_fasta, "r") as fh1, open(test_data_dir / "INSC1003.fa",
"r") as fh2:
assert fh1.read() == fh2.read()
def test_genbank_to_gff(self, test_data_dir, tmp_path, gbk, gff3, add_sequences):
"""
INSC1006_chrI.gff3 and INSC1003.gff3 were created from INSC1006_chrI.gbff and INSC1003.gbk
respectively, so we can compare to the source file.
"""
gbk = test_data_dir / gbk
with open(gbk, "r") as fh:
parsed = list(ParsedAnnotationRecord.parsed_annotation_records_to_model(parse_genbank(fh)))
tmp_gff = tmp_path / "tmp.gff"
with open(tmp_gff, "w") as fh:
collection_to_gff3(parsed, fh, add_sequences=add_sequences)
for l1, l2 in zip(open(tmp_gff), open(test_data_dir / gff3)):
assert l1 == l2
def test_tbl_export_from_genbank(test_data_dir, tmp_path, genbank,
expected_tbl):
genbank = test_data_dir / genbank
recs = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(genbank)))
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_collection_to_fasta_from_genbank(test_data_dir, tmp_path):
"""This FASTA export matches exactly because there are no FASTA comments."""
gbk = test_data_dir / "INSC1006_chrI.gbff"
with open(gbk, "r") as fh:
parsed = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh)))
tmp_fasta = tmp_path / "tmp.fasta"
with open(tmp_fasta, "w") as fh:
collection_to_fasta(parsed, fh)
with open(tmp_fasta, "r") as fh1, open(test_data_dir / "INSC1006_chrI.fa",
"r") as fh2:
assert fh1.read() == fh2.read()
def test_records_to_fasta_from_genbank(test_data_dir, tmp_path):
"""INSC1006_chrI.gbff will have FASTA comments when exported by BioPython,
and so the sequence will match but the comments will be lost."""
gbk = test_data_dir / "INSC1006_chrI.gbff"
with open(gbk, "r") as fh:
parsed = parse_genbank(fh)
tmp_fasta = tmp_path / "tmp.fasta"
with open(tmp_fasta, "w") as ofh:
for rec in parsed:
rec.to_fasta(ofh)
with open(tmp_fasta, "r") as fh1, open(test_data_dir / "INSC1006_chrI.fa",
"r") as fh2:
f1 = fh1.readlines()
f2 = fh2.readlines()
assert f1[1:] == f2[1:]
assert f1[0] != f2[0]
assert f1[0].split()[0] == f2[0].split()[0]
def test_collection_to_fasta_from_genbank_fasta_header(test_data_dir,
tmp_path):
"""INSC1003.fa has FASTA comments, and so the sequence will match but the comments will be lost."""
gbk = test_data_dir / "INSC1003.gbk"
with open(gbk, "r") as fh:
parsed = list(
ParsedAnnotationRecord.parsed_annotation_records_to_model(
parse_genbank(fh)))
tmp_fasta = tmp_path / "tmp.fasta"
with open(tmp_fasta, "w") as fh:
collection_to_fasta(parsed, fh)
with open(tmp_fasta, "r") as fh1, open(test_data_dir / "INSC1003.fa",
"r") as fh2:
f1 = fh1.readlines()
f2 = fh2.readlines()
assert f1[1:] == f2[1:]
assert f1[0] != f2[0]
assert f1[0].split()[0] == f2[0].split()[0]
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)