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A python package for Personalized Genomics and Proteomics

Project description

Short description:

pyGeno is developed by Tariq Daouda at the Institute for Research in Immunology and Cancer (IRIC).

With pyGeno you can do that:

from pyGeno.Genome import *

#load a genome
ref = Genome(name = 'GRCh37.75')
#load a gene
gene = ref.get(Gene, name = 'TPST2')[0]
#print the sequences of all the isoforms
for prot in gene.get(Protein) :
 print prot.sequence

You can also do it for the specific genomes of your subjects:

pers = Genome(name = 'GRCh37.75', SNPs = ["RNA_S1"], SNPFilter = myFilter())

And much more: https://github.com/tariqdaouda/pyGeno

Verbose Description

pyGeno is a python package that allows you to easily combine Reference Genomes and sets of Polymorphisms together to create personalized genomes. Personalized genomes can be used to work directly on the genomes of you subjects and be translated into Personalized Proteomes,

Multiple sets of of polymorphisms can also be combined together to leverage their independent benefits ex:

RNA-seq and DNA-seq for the same individual to improve the coverage RNA-seq of an individual + dbSNP for validation Combine the results of RNA-seq of several individual to create a genome only containing the common polymorphisms pyGeno is also a personal database that give you access to all the information provided by Ensembl (for both Reference and Personalized Genomes) without the need of queries to distant HTTP APIs. Allowing for much faster and reliable genome wide study pipelines.

It also comes with parsers for several file types and various other useful tools.

Full Documentation

The full documentation is available here

If you like pyGeno, please let me know. For the latest news, you can follow me on twitter @tariqdaouda.

Project details


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