plastid.readers package

Package overview

This package contains parsers for various file types. All parsers behave as iterators, and return data that is standarized to 0-indexed, half-open coordinate systems, in keeping with Python conventions. In addition, all of the annotation file readers (except BigBed) are compatible with tabix compression, which is supported via Pysam.

Helper code can be found in the following modules:

Module Contents
plastid.readers.common Helper functions used by many annotation file readers
plastid.readers.gff_tokens Functions for parsing and exporting attributes in the ninth column of GTF2 and GFF3 files