A python package for Personalized Medicine and Proteogenomics
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') #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
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.
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