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.sequenceYou 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
pyGeno is a personal bioinformatic database that runs directly into python, on your laptop and does not depend upon any REST API. pyGeno is here to make extracting data such as gene sequences a breeze, and is designed to be able cope with huge queries. The most exciting feature of pyGeno, is that it allows to work with seamlessly with both reference and Presonalized Genomes.
Personalized Genomes, are custom genomes that you create by combining a reference genome, sets of polymorphims and an optional filter. pyGeno will take care of applying the filter and inserting the polymorphisms at their right place, so you get direct access to the DNA and Protein sequences of your patients.
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.
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.