plastid package¶
Welcome to plastid!
This package contains various utilities for analyzing high-throughput sequencing data, with an emphasis on simplicity for users. To this end, this package provides:
A set of command-line scripts that implement common sequencing workflows (see
plastid.bin
).Readers that abstract data from various file formats into a minimal set of object types. These object types define APIs that easily interface with existing scientific tools, such as the SciPy stack (see
plastid.genomics
andplastid.readers
)Tools to facilitate writing command-line scripts (see
plastid.util.scriptlib
)
Package overview¶
plastid is divided into the following subpackages:
Package
Contents
Command-line scripts
Classes and functions to manipulate genome annotations, alignments, and quantitative data
Tools for plotting
Parsers for various file formats
Utilities (e.g. function decorators, exceptions, argument parsers)
plastid.test
Unit and functional tests (requires download of test datasets)
Subpackages¶
- plastid.bin package
- Submodules
- plastid.bin.counts_in_region module
- plastid.bin.crossmap module
- plastid.bin.cs module
- plastid.bin.findjuncs module
- plastid.bin.get_count_vectors module
- plastid.bin.gff_parent_types module
- plastid.bin.make_wiggle module
- plastid.bin.metagene module
- plastid.bin.phase_by_size module
- plastid.bin.psite module
- plastid.bin.reformat_transcripts module
- plastid.bin.slidejuncs module
- plastid.bin.test_table_equality module
- Submodules
- plastid.genomics package
- Package overview
- Submodules
- plastid.genomics.c_common module
- plastid.genomics.c_common module
- plastid.genomics.c_common module
- plastid.genomics.genome_array module
- plastid.genomics.genome_hash module
- plastid.genomics.map_factories module
- plastid.genomics.map_factories module
- plastid.genomics.map_factories module
- plastid.genomics.roitools module
- plastid.genomics.roitools module
- plastid.genomics.roitools module
- plastid.genomics.seqtools module
- plastid.genomics.splicing module
- plastid.plotting package
- plastid.readers package
- Package overview
- 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
- plastid.util package