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gtf_to_genes 1.09

Fast GTF parser

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Overview
***************************************
    We want an extremely fast, lightweight way to access gene data stored in GTF format.

    The parsed data is held in an intuitive
        Gene
             -> transcript
             -> transcript
        with exons being stored as intervals

    Our aim is to
       * cache data in binary format, which can be
       * re-read in < 10s for even the largest genomes

    Currently initial parsing Ensembl Homo sapiens release 56 takes around 4.5 minutes.
    The binary data can be reloaded in < 10s.
    This contains *all* of the data structure in the original GTF file

    Note that we sacrifice memory usage for speed. This is seldom a problem for modern computers
    and genome sizes (There are around ~400,000 exons but there are stored as intervals / int pairs)

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A Simple example
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    ::
        gene_structures = t_parse_gtf("Mus musculus")

        #
        #   used cached data for speed
        #
        ignore_cache = False

        #
        #   get all protein coding genes only
        #
        genes_by_type = gene_structures.get_genes(gtf_file, logger, ["protein_coding"], ignore_cache = ignore_cache)

        #
        #   print out gene counts
        #
        t_parse_gtf.log_gene_types (logger, genes_by_type)

        return genes_by_type
 
File Type Py Version Uploaded on Size
gtf_to_genes-1.09.tar.gz (md5) Source 2012-07-12 23KB
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