GFF3 - Classes, functions and iterators for working with GFF3 files

This module mostly inherits from the GTF and replaces selected functionality to allow working with GFF3 formatted files.

class GFF3.Entry

Bases: cgat.GTF.Entry

representation of a GFF3 formatted entry.

This class inherits from GTF.Entry, but changes the parsing to reflect GFF3.

parseInfo(attributes, line=None)

Parse the attributes line of an entry, line parameter provided purely for backwards compatability

getAttributeField()

return the attributes field as a ; delimied field

GFF3.flat_file_iterator(infile)

simple iterator that iterators over lines in a field and yeilds GFF3 Entry objects

GFF3.iterator_from_gff(gff_iterator)

to make this slot in with other gtf using scripts, allow copying of an entry into gff3 format. Acts via str, probably not the most efficient way to do things

GFF3.chrom_iterator(gff3_iterator)

takes a an iterator and returns an iterator over iterators, with a new instance every time a new chromosome is found