pyGeno 1.1.5

A python package for Personalized Proteogenomics

Short description:

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 mainly intended for personal medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations, 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 human’s specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of python, a general programming language. It’s range of application therefore encompasses both short scripts and large scale genome-wide studies.