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bunbun/gtf-to-genes
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gtf_to_genes is a Python parser which caches all the genes / transcripts from a GTF file and caches the data into python classes for high speed access. The initial parsing and indexing of a GTF file is a slow process, taking over a minute. But once that is done, the genes and transcripts can be retrieved in seconds. Exons are stored efficiently per gene with each transcript only having indices into these exon lists array.array are used as much as possible for speed and efficiency. To install run: python ./setup.py install or easy_install -U gtf_to-genes TODO: * __str()__ should show exons rather than indices into parent's exons
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