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pyVEP
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Python interface to Variant Effect Predictor
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Download README
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pyVEP
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# pyVEP Python interface to Variant Effect Predictor pyVEP is a python tool to access [Variant Effect Predictor](http://www.ensembl.org/info/docs/tools/vep/index.html). 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: ```python 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 ```bash python setup.py install ``` ### License The MIT License ### Contact [alexandros.kanterakis@gmail.com](alexandros.kanterakis@gmail.com)
