bgvep 0.3

Installation

This project is a Python package and can be installed with pip. Download the source code, get into this project directory and execute:

pip install .

Usage

To request the output of 1 or more positions, simply indicate the chromosome, the initial and the final positions you are interested.

bgvep --genome hg19 --vep 88 --chromosome chr1 --begin 100000 --end 100004

from bgvep import get
for data in get('hg19', '88', 'chr1', 100000, 100004):
    ...

from bgvep.readers import Tabix

with Tabix('hg19', '88') as reader:
     for data in reader.get('chr1', 100000, 100004):
          ...

The output

The format of the output is:

• Chromosome

• Position

• Reference

• Alternate

• Gene

• Feature

• Feature_type

• Consequence

• cDNA_position

• CDS_position

• Protein_position

• Amino_acids

• Codons

• Existing_variation

• Impact

• Distance

• Strand

• Flags

• Symbol

• Symbol source

• HGNC_ID

• Canonical

• ENSP

When asking for the most-severe consquence type, the output is formed by the most severe consequente type of all the possible changes of the reference allele. The order is always ACGT, and if the refernce allele changes to itself, nothing is returned for it.

Support

If you are having issues, please let us know. You can contact us at: bbglab@irbbarcelona.org