Classes and functions for gff annotation parsing

common.parsing_routines.gff_gtf_tools.py

This module contains routines for reading, parsing and summarizing data in gft and gff files. There are at least three versions of the gff format (so this will be fun!) and then gtf (v2.2). This is a good page for information about the versions: http://www.broadinstitute.org/igv/GFF

module_version:1.0 created_on:2013-11-27

gff and gtf tools

class parsing_routines.gff_gtf_tools.annotation(fname, skip_fasta=True, filetype=None, verbose=False)

A simple class for representing annotations from a gff or gtf file

parsing_routines.gff_gtf_tools.parse_gff_v3(fname, skip_fasta=True, force_type=None, progress_report=False)

read a gff_v3 file and convert it into a set of ‘regions’

skip_fasta controls what to do with fasta sequences storred at the end of gff files, force_type controls whether to autodetect the type from the gff file or whether to assume a known filetype.