------------------------------
Changes here are mostly under the hood, involving improvements in usability,
speed, stability, compatibility, and error reporting. We also fixed up tools
for developers and added entrypoints for custom mapping rules.
Added
.....
- Users can now control verbosity/frequency of warnings via '-v' or '-q'
options! By default there should no long screens of DataWarnings
when processing Ensembl (or other) GTFs.
- ``--aggregate`` option added to ``psite`` script to improve sensitivity
for low-count data.
- Created entrypoints for allowing users to use custom mapping rules
in the command line scripts:
- ``plastid.mapping_rules`` for specifying new mapping functions
- ``plastid.mapping_options`` for specifying any other command-line
arguments they consume
Detailed instructions for use in the *developer info* section
of `<plastid.readthedocs.org>`_.
- Argument parsing classes that replace methods deprecated below:
- :class:`~plastid.util.scriptlib.argparsers.AlignmentParser`
- :class:`~plastid.util.scriptlib.argparsers.AnnotationParser`
- :class:`~plastid.util.scriptlib.argparsers.MaskParser`
- :class:`~plastid.util.scriptlib.argparsers.SequenceParser`
- :class:`~plastid.util.scriptlib.argparsers.PlottingParser`
Fixed
.....
- updated plotting tools to fetch color cycles from matplotlib versions >= 1.5
as well as >= 1.3. This corrected a plotting bug in `cs`.
- :meth:`AnnotationParser.get_genome_hash_from_args` now internally uses
GFF3_Reader and GTF2_Reader instead of GFF3_TranscriptAssembler and
GTF2_TranscriptAssembler, allowing mask files in GTF2/GFF3 foramts
to be type-agnostic in command-line scripts
- contig names no longer lost when using 2bit files in `crossmap`
- updates to :mod:`~plastid.bin.psite`
- output header in metagene profiles. Sorry about that
- fix compatibility problem with new versions of matplotlib
- now catches a ``ValueError`` that used to be an ``IndexError``
in earlier versions of :mod:`numpy`.
- Fixed loss-of-ID bug in :meth:`Transcript.get_cds`
Changed
.......
- :func:`~plastid.util.services.decorators.deprecated` function decorator
now optionally takes parameters indicating the future version of plastid
in which deprecated features will be removed, and what replacement to use
instead
Deprecated
..........
- Argument parsing methods:
- ``get_alignment_file_parser()`` & ``get_genome_array_from_args()``.
Use :class:`~plastid.util.scriptlib.argparsers.AlignmentParser` instead.
- ``get_annotation_file_parser()`` & ``get_transcripts_from_args()``,
``get_segmentchain_file_parser()`` & ``get_segmentchains_from_args()``
Use :class:`~plastid.util.scriptlib.argparsers.AnnotationParser` instead.
- ``get_mask_file_parser()`` & ``get_genome_hash_from_mask_args()``.
Use :class:`~plastid.util.scriptlib.argparsers.MaskParser` instead.
- ``get_sequence_file_parser()`` & ``get_seqdict_from_args()``.
Use :class:`~plastid.util.scriptlib.argparsers.SequenceParser` instead
- ``get_plotting_parser()``, ``get_figure-from_args()``, & ``get_colors_from_args``.
Use :class:`~plastid.util.scriptlib.argparsers.PlottingParser` instead