pyVEP

Python interface to Variant Effect Predictor

pyVEP is a python tool to access Variant Effect Predictor. It does not rely on a specific API and it just emulates a GET request to the "Instant result for first variant" feature of VEP.

Example:

from pyVEP import VEP

r = VEP('9:g.22125504G>C', 'grch38')
print r[0]['most_severe_consequence']
"downstream_gene_variant"

VEP also accepts the following parameters:

• assembly. REQUIRED. Sets the version of he human reference assemby. Acceptable values are: grch37, grch38, hg19 and hg18. Default value is grch38.
• variant_type . In general, pyVEP applies some heuristics in order to guess the variant type (if it is ensembl, vcf, hgvs, or variant identifier). Set the variant_type parameter to skip this step. Available values are: region for VCF and Ensembl default, hgvs for HGVS nomenclature and id for variant identifier (ex. rs variant).

According to VEP (http://asia.ensembl.org/Tools/VEP) it accepts variants in any of the following forms:

• Ensembl default:

1 182712 182712 A/C 1
2 265023 265023 C/T 1
3 319781 319781 A/- 1
19 110748 110747 -/T 1
1 160283 471362 DUP 1
1 1385015 1387562 DEL 1

• VCF:

1 182712 . A C . . .
3 319780 . GA G . . .
19 110747 . G GT . . .
1 160283 sv1 . <DUP> . . SVTYPE=DUP;END=471362 .
1 1385015 sv2 . <DEL> . . SVTYPE=DEL;END=1387562 .

• Variant identifiers:

rs699
rs144678492
COSM354157

• HGVS notations:

AGT:c.803T>C
9:g.22125504G>C
ENST00000003084:c.1431_1433delTTC
19:g.110747_110748insT
LRG_101t1:c.1019T>C

• Pileup
  • Pileup is not supported on the "Instant result for first variant" functionality.

Install

python setup.py install 

License

The MIT License

Contact

alexandros.kanterakis@gmail.com