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BBGLab tool

Project description

Read data generated within the bgvep project. Within that project there are two datasets, both identified by the reference genome (e.g. hg19) and the VEP version (e.g. 88):

  • a tabix file with the run of vep for all positions in the genome
  • a bgpack file with only the most severe consequence type.

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.

Commad line usage

Execute bgvep --help for getting all the information.

The output is printed to the screen using tabs as separators for the indexes:

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

Adding the --most-severe flags, returns the most severe consequence type for the 3 possible changes of the allele in that position.

Python usage

The easiest way to use bgvep is to make use of the generators get and get_most_severe.

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

However, the best way to use bgvep is using directly the readers: the Tabix and the BGPack readers, which are context managers.

from bgvep.readers import Tabix

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

The advantage of using directly the readers is that they are not instantiated on every call.

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

Project details


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