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.
Annotation files
BED and Extended BED formats
PSL (BLAT format)
Alignment & count files
bowtie alignment
Miscellaneous
Helper code can be found in the following modules:
Submodules¶
- plastid.readers.autosql module
- plastid.readers.bbifile module
- plastid.readers.bbifile module
- plastid.readers.bbifile module
- plastid.readers.bed module
- plastid.readers.bigbed module
- plastid.readers.bigbed module
- plastid.readers.bigbed module
- plastid.readers.bigwig module
- plastid.readers.bigwig module
- plastid.readers.bigwig module
- plastid.readers.bowtie module
- plastid.readers.common module
- plastid.readers.gff module
- plastid.readers.gff_tokens module
- plastid.readers.psl module
- plastid.readers.wiggle module