def test_get_genes(cyvcf2_variant):
csq_entry = "C|missense_variant|MODERATE|POC1A|ENSG00000164087|"\
"Transcript|ENST00000296484|protein_coding|4/11||ENST00000296484.2"\
":c.322A>G|ENSP00000296484.2:p.Ser108Gly|362|322|108|S/G|Agt/Ggt"\
"|||-1|HGNC|24488||CCDS2846.1|ENSP00000296484|POC1A_HUMAN|"\
"B2RDV4_HUMAN|UPI000045711C|deleterious|possibly_damaging|"\
"PROSITE_profiles:PS50082&PROSITE_profiles:PS50294&hmmpanther"\
":PTHR22847:SF319&hmmpanther:PTHR22847&Gene3D:2.130.10.10&"\
"Pfam_domain:PF00400&SMART_domains:SM00320&Superfamily_domains:"\
"SSF50978|||||,C|missense_variant|MODERATE|POC1A|ENSG00000164087"\
"|Transcript|ENST00000394970|protein_coding|4/10||"\
"ENST00000394970.2:c.322A>G|ENSP00000378421.2:p.Ser108Gly|640"\
"|322|108|S/G|Agt/Ggt|||-1|HGNC|24488||CCDS54592.1|ENSP00000378421"\
"|POC1A_HUMAN||UPI00006633C6|deleterious|benign|"\
"Superfamily_domains:SSF50978&SMART_domains:SM00320&Pfam_domain"\
":PF00400&Gene3D:2.130.10.10&hmmpanther:PTHR22847&hmmpanther:"\
"PTHR22847:SF319&PROSITE_profiles:PS50082&PROSITE_profiles:PS50294"\
"|||||,C|missense_variant|MODERATE|POC1A|ENSG00000164087|"\
"Transcript|ENST00000474012|protein_coding|4/11||ENST00000474012"\
".1:c.208A>G|ENSP00000418968.1:p.Ser70Gly|425|208|70|S/G|Agt"\
"/Ggt|||-1|HGNC|24488||CCDS54591.1|ENSP00000418968|POC1A_HUMAN|"\
"B2RDV4_HUMAN|UPI0000E1FCF5|tolerated|possibly_damaging|Superfami"\
"ly_domains:SSF50978&SMART_domains:SM00320&Gene3D:2.130.10.10&"\
"Pfam_domain:PF00400&hmmpanther:PTHR22847:SF319&hmmpanther:"\
"PTHR22847&PROSITE_profiles:PS50294&PROSITE_profiles:PS50082|||||"
csq_header = "Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|"\
"Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|"\
"Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|"\
"STRAND|SYMBOL_SOURCE|HGNC_ID|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|"\
"SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|"\
"MOTIF_SCORE_CHANGE"
header = [word.upper() for word in csq_header.split('|')]
## GIVEN a variant with vep annotation and a vep header
raw_transcripts = (
dict(
zip(
header,
csq_entry.split('|')
)
)
for transcript_info in csq_entry.split(',')
)
parsed_transcripts = []
for parsed_transcript in parse_transcripts(raw_transcripts, allele='C'):
parsed_transcripts.append(parsed_transcript)
# variant = cyvcf2_variant
# variant.INFO['CSQ'] = csq_entry
genes = parse_genes(parsed_transcripts)
for gene in genes:
assert gene['hgnc_id'] == 24488
assert len(genes) == 1
def test_get_genes(cyvcf2_variant):
csq_entry = (
"C|missense_variant|MODERATE|POC1A|ENSG00000164087|"
"Transcript|ENST00000296484|protein_coding|4/11||ENST00000296484.2"
":c.322A>G|ENSP00000296484.2:p.Ser108Gly|362|322|108|S/G|Agt/Ggt"
"|||-1|HGNC|24488||CCDS2846.1|ENSP00000296484|POC1A_HUMAN|"
"B2RDV4_HUMAN|UPI000045711C|deleterious|possibly_damaging|"
"PROSITE_profiles:PS50082&PROSITE_profiles:PS50294&hmmpanther"
":PTHR22847:SF319&hmmpanther:PTHR22847&Gene3D:2.130.10.10&"
"Pfam_domain:PF00400&SMART_domains:SM00320&Superfamily_domains:"
"SSF50978|||||,C|missense_variant|MODERATE|POC1A|ENSG00000164087"
"|Transcript|ENST00000394970|protein_coding|4/10||"
"ENST00000394970.2:c.322A>G|ENSP00000378421.2:p.Ser108Gly|640"
"|322|108|S/G|Agt/Ggt|||-1|HGNC|24488||CCDS54592.1|ENSP00000378421"
"|POC1A_HUMAN||UPI00006633C6|deleterious|benign|"
"Superfamily_domains:SSF50978&SMART_domains:SM00320&Pfam_domain"
":PF00400&Gene3D:2.130.10.10&hmmpanther:PTHR22847&hmmpanther:"
"PTHR22847:SF319&PROSITE_profiles:PS50082&PROSITE_profiles:PS50294"
"|||||,C|missense_variant|MODERATE|POC1A|ENSG00000164087|"
"Transcript|ENST00000474012|protein_coding|4/11||ENST00000474012"
".1:c.208A>G|ENSP00000418968.1:p.Ser70Gly|425|208|70|S/G|Agt"
"/Ggt|||-1|HGNC|24488||CCDS54591.1|ENSP00000418968|POC1A_HUMAN|"
"B2RDV4_HUMAN|UPI0000E1FCF5|tolerated|possibly_damaging|Superfami"
"ly_domains:SSF50978&SMART_domains:SM00320&Gene3D:2.130.10.10&"
"Pfam_domain:PF00400&hmmpanther:PTHR22847:SF319&hmmpanther:"
"PTHR22847&PROSITE_profiles:PS50294&PROSITE_profiles:PS50082|||||"
)
csq_header = (
"Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|"
"Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|"
"Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|"
"STRAND|SYMBOL_SOURCE|HGNC_ID|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|"
"SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|"
"MOTIF_SCORE_CHANGE"
)
header = [word.upper() for word in csq_header.split("|")]
## GIVEN a variant with vep annotation and a vep header
raw_transcripts = (
dict(zip(header, csq_entry.split("|")))
for transcript_info in csq_entry.split(",")
)
parsed_transcripts = []
for parsed_transcript in parse_transcripts(raw_transcripts, allele="C"):
parsed_transcripts.append(parsed_transcript)
# variant = cyvcf2_variant
# variant.INFO['CSQ'] = csq_entry
genes = parse_genes(parsed_transcripts)
for gene in genes:
assert gene["hgnc_id"] == 24488
assert len(genes) == 1
def test_get_genes(cyvcf2_variant):
csq_entry = "C|missense_variant|MODERATE|POC1A|ENSG00000164087|"\
"Transcript|ENST00000296484|protein_coding|4/11||ENST00000296484.2"\
":c.322A>G|ENSP00000296484.2:p.Ser108Gly|362|322|108|S/G|Agt/Ggt"\
"|||-1|HGNC|24488||CCDS2846.1|ENSP00000296484|POC1A_HUMAN|"\
"B2RDV4_HUMAN|UPI000045711C|deleterious|possibly_damaging|"\
"PROSITE_profiles:PS50082&PROSITE_profiles:PS50294&hmmpanther"\
":PTHR22847:SF319&hmmpanther:PTHR22847&Gene3D:2.130.10.10&"\
"Pfam_domain:PF00400&SMART_domains:SM00320&Superfamily_domains:"\
"SSF50978|||||,C|missense_variant|MODERATE|POC1A|ENSG00000164087"\
"|Transcript|ENST00000394970|protein_coding|4/10||"\
"ENST00000394970.2:c.322A>G|ENSP00000378421.2:p.Ser108Gly|640"\
"|322|108|S/G|Agt/Ggt|||-1|HGNC|24488||CCDS54592.1|ENSP00000378421"\
"|POC1A_HUMAN||UPI00006633C6|deleterious|benign|"\
"Superfamily_domains:SSF50978&SMART_domains:SM00320&Pfam_domain"\
":PF00400&Gene3D:2.130.10.10&hmmpanther:PTHR22847&hmmpanther:"\
"PTHR22847:SF319&PROSITE_profiles:PS50082&PROSITE_profiles:PS50294"\
"|||||,C|missense_variant|MODERATE|POC1A|ENSG00000164087|"\
"Transcript|ENST00000474012|protein_coding|4/11||ENST00000474012"\
".1:c.208A>G|ENSP00000418968.1:p.Ser70Gly|425|208|70|S/G|Agt"\
"/Ggt|||-1|HGNC|24488||CCDS54591.1|ENSP00000418968|POC1A_HUMAN|"\
"B2RDV4_HUMAN|UPI0000E1FCF5|tolerated|possibly_damaging|Superfami"\
"ly_domains:SSF50978&SMART_domains:SM00320&Gene3D:2.130.10.10&"\
"Pfam_domain:PF00400&hmmpanther:PTHR22847:SF319&hmmpanther:"\
"PTHR22847&PROSITE_profiles:PS50294&PROSITE_profiles:PS50082|||||"
csq_header_line = "Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|"\
"Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|"\
"Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|"\
"STRAND|SYMBOL_SOURCE|HGNC_ID|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|"\
"SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|"\
"MOTIF_SCORE_CHANGE"
## GIVEN a variant with vep annotation and a vep header
variant = cyvcf2_variant
variant.INFO['CSQ'] = csq_entry
csq_header = csq_header_line.split('|')
genes = parse_genes(variant.INFO.get('CSQ'), csq_header)
for gene in genes:
assert gene['hgnc_id'] == 24488
assert len(genes) == 1