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A python package for Personalized Medicine and Proteogenomics

Project description

Short description:

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

pyGeno is your best friend. It’s here so you can easily take advantage of both reference sequences and annotations form Ensembl, and your favorite sets of polymorphisms. Currently pyGeno supports dbSNP and SNPs derived from Illumina’s Casava pipeline.

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 mainly intended for personalized medicine, but it can serve many purposes. It integrates reference sequences and annotations for Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory- efficient and fast framework, therefore allowing the user to easily explore reference and custom genomes and proteomes. pyGeno can be used for both short scripts and large scale genome-wide studies.

Full Documentation

The full documentation is available here

For the latest news about pyGeno, you can follow me on twitter @tariqdaouda.

Project details


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