def test_get_transcript_and_mutate_vcf():
variant = {
'chr' : '10',
'pos' : 43617416,
'ref' : 'T',
'alt' : 'C'
}
vcf = pd.DataFrame.from_records([variant])
transcripts_ids = ensembl.annotate_vcf_transcripts(vcf)
transcript_ids = set(transcripts_ids['stable_id_transcript'])
assert( "ENST00000355710" in transcript_ids)
assert( "ENST00000340058" in transcript_ids)
transcript_id = "ENST00000355710"
cdna_idx = ensembl.get_transcript_index_from_pos(
variant['pos'], transcript_id, skip_untranslated_region = False)
assert cdna_idx is not None
assert cdna_idx < 5569
cdna_transcript = ref_data.get_cdna(transcript_id)
assert(cdna_transcript[cdna_idx] == variant['ref'])
cds_idx = ensembl.get_transcript_index_from_pos(
variant['pos'], transcript_id, skip_untranslated_region = True)
assert cds_idx is not None
cds_transcript = ref_data.get_cds(transcript_id)
assert(cds_transcript[cds_idx] == variant['ref'])
region = mutate_protein_from_transcript(
cds_transcript,
cds_idx,
variant['ref'],
variant['alt'],
padding = 10)
assert region is not None
assert len(region.seq) == 21, (region.seq, len(region.seq))
assert region.seq == 'RSQGRIPVKWTAIESLFDHIY'
def test_get_transcript_index_from_pos():
variant = {
'chr' : '3',
'pos' : 41275636,
'ref' : 'G',
'alt' : 'A'
}
transcript_id = 'ENST00000405570'
idx = ensembl.get_transcript_index_from_pos(
41275636, transcript_id, skip_untranslated_region = False)
assert(idx == 1686), idx
transcript = ref_data.get_cdna(transcript_id)
assert(transcript[idx] == variant['ref'])
def test_peptide_from_transcript_PARS2():
"""
test_peptide_from_transcript:
"""
transcript_id = 'ENST00000371279'
variant = {
'chr' : '1',
'pos' : 55224569,
'ref' : 'T',
'alt' : 'G'
}
cds_idx = ensembl.get_transcript_index_from_pos(
variant['pos'], transcript_id, skip_untranslated_region = True)
assert cds_idx is not None
assert cds_idx == 265
