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On-disk gene database searchable using an interval tree

Project Description

# PyGenes

PyGenes is an on disk searchable gene database for python, implemented in c++ for speed. The current implementation is primarily aimed at providing an interface for ensembl gtf files.

## Usage

Create a pygenes database and load from an ensembl gtf file:

gene_models = pygenes.GeneModels()

The database can be serialized to a binary format:


gene_models2 = pygenes.GeneModels()

Get a gene by gene id:

gene = gene_models.get_gene('ENSG00000101596')

Find either overlapping or contained genes within a region:

gene_models.find_overlapping_genes('18', 2700000, 2800000)
gene_models.find_contained_genes('18', 2700000, 2800000)

Calculate the location in the gene as one of 'utr3p', 'coding', 'intron', 'utr5p', 'upstream', 'downstream', 'utr':

gene_models.calculate_gene_location('ENSG00000101596', 2792681)

Calculate the location in the genome of a position in a transcript:

gene_models.calculate_genomic_position('ENST00000320876', 461)

Calculate the regions in the genome of a region in a transcript:

gene_models.calculate_genomic_regions('ENST00000320876', 461, 796)

Release History

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Source None Feb 24, 2016

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