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
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getAttributeField
()¶ return the attributes field as a ; delimied field
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GFF3.
flat_file_iterator
(infile)¶ simple iterator that iterators over lines in a field and yeilds GFF3 Entry objects
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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
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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