------------------------------
First release under official name!
Added
.....
- Major algorithmic improvements to internals & command-line scripts
Changed
.......
- Reimplemented mapping rules and some internals in Cython, giving 2-10x
speedup for some operations
- ``GenomicSegment`` now sorts lexically. Properties are read-only
.. note::
This project was initially developed internally under the provisional name
``genometools``, and then later under the codename ``yeti``. The current
name, ``plastid`` will not change. Changelogs from earlier versions
appear below.
yeti [0.2.1] = [2015-09-06]
---------------------------
Added
.....
- Support for extended BED formats now in both import & export, in
command-line scripts and interactively
- BED Detail format and known ENCODE BED subtypes now automatically parsed
from track definition lines
- Created warning classes DataWarning, FileFormatWarning, and ArgumentWarning
- parallelized `crossmap` script
- command line support for more sequence file formats; and a sequence
argparser
Changed
.......
- speed & memory optimizations for `cs generate` script, resulting in 90%
memory reduction on human genome annotation GrCh38.78
- ditto `metagene generate` script
- `crossmap` script does not save kmer files unless --save_kmers is given
- warnings now given at first (instead of every) occurence
- lazy imports; giving speed improvements to command-line scripts
yeti [0.2.0] = [2015-08-26]
---------------------------
**Big changes,** including some that are **backwards-incompatible.** We
really think these are for the best, because they improve compatibility
with other packages (e.g. pandas) and make the package more consistent
in design & behavior
Added
.....
- GenomeArray __getitem__ and __setitem__ now can take SegmentChains as
arguments
- Mapping functions for bowtie files now issue warnings when reads are
unmappable
- support for 2bit files (via twobitreader) and for dicts of strings in
SegmentChain.get_sequence
- various warnings added
Changed
.......
- pandas compatibility: header rows in all output files no longer have
starting '. meaning UPDATE YOUR OLD POSITIONS/ROI FILES
- __getitem__ from GenomeArrays now returns vectors 5' to 3' relative to
GenomicSegment rather than to genome. This is more consistent with user
expectations.
- _get_valid_X methods of SegmentChain changed to _get_masked_X for
consistency with documentation and with numpy notation
Removed
.......
- ArrayTable class & tests
yeti [0.1.1] = [2015-07-23]
---------------------------
Added
.....
- Created & backpopulated changelog
- Docstrings re-written for user rather than developer focus
- AssembledFeatureReader
- Complete first draft of user manual documentation
- Readthedocs support for documentation
- GFF3_TranscriptAssembler now also handles features whose subfeatures share
`ID` attributes instead of `Parent` attributes.
Changed
.......
- import of scientific packages now simulated using `mock` during
documentation builds by Sphinx
- duplicated attributes in GTF2 column 9 are now catenated & returned as a
list in attr dict. This is outside GTF2 spec, but a behavior used by
GENCODE
Fixed
.....
- Removed bug from :func:`yeti.bin.metagene.do_generate` that extended
maximal spanning windows past equivalence points in 3' directions. Added
extra unit test cases to suit it.
- GenomeHash can again accept GenomicSegments as parameters to __getitem__.
Added unit tests for this.
Removed
.......
- Removed deprecated functions, modules, & classes:
- GenomicFeature
- BED_to_Transcripts
- BigBed_to_Transcripts
- GTF2_to_Transcripts
- GFF3_to_Transcripts
- TagAlignReader
yeti [0.1.0] = [2015-06-06]
---------------------------
First internal release of project under new codename, ``yeti``. Reset version
number.
Added
.....a
- AssembledFeatureReader, GTF2_TranscriptAssembler, GFF3_TranscriptAssembler
- GTF2/GFF3 token parsers now issue warnings on repeated keys
- GFF3 token parsers now return 'Parent', 'Alias', 'Dbxref', 'dbxref', and
'Note' fields as lists
Changed
.......
- Package renamed from ``genometools`` to its provisional codename ``yeti``
- Reset version number to 0.1.0
- Refactored existing readers to descent from AssembledFeatureReader
- Migration from old SVN to GIT repo
- Renaming & moving of functions, classes, & modules for consistency and to
avoid name clashes with other packages
================================== ====================================
Old name New Name
---------------------------------- ------------------------------------
GenomicInterva GenomicSegment
IVCollection SegmentChain
NibbleMapFactory CenterMapFactory
genometools.genomics.ivtools yeti.genomics.roitools
genometools.genomics.readers yeti.readers
genometools.genomics.scriptlib yeti.util.scriptlib
================================== ====================================
genometools [0.9.1] - 2015-05-21
--------------------------------
Changed
.......
- renamed suppress_stdr -> capture_stderr
Added
.....
- capture_stdout decorator
genometools [0.9.0] - 2015-05-20
--------------------------------
Changed
.......
- All functions that used GenomicFeatures now use IVCollections instead
Removed
.......
- GenomicFeature support from GenomeHash subclasses
- GenomicFeature support from IVCollection and GenomicInterval overlap end
quality criteria
Deprecated
..........
- GenomicFeature
genometools [0.8.3] - 2015-05-19
--------------------------------
Added
.....
- Included missing `.positions` and `.sizes` files into egg package
genometools [0.8.2] - 2015-05-19
--------------------------------
Changed
.......
- Test data now packaged in eggs
- updated documentation
Fixed
.....
- Bug in cleanup for test_crossmap
- Bug in setup.py
genometools [0.8.1] - 2015-05-18
--------------------------------
Added
.....
- Python 3.0 support
- Support for tabix-compressed files. Creation of TabixGenomeHash
Changed
.......
- Propagate various attributes to sub-features (utr_ivc, CDS) from Transcript
- Propagate all attributes to sub-features during GTF export from Transcript
- GTF2 export of Transcript objects now generates 'start_codon' and
'stop_codon' features
- Update of setup.py and Makefile to make dev vs distribution eggs
- 'transcript_ids' column of 'cs generate' position file now sorted before
comma join.
genometools [0.8.2015-05-08] - 2015-05-08
-----------------------------------------
Changed
.......
- Merger of `make_tophat_juncs`, `find_juncs`, and `merge_juncs` into one
script
- Standardization of column names among various output files: region,
regions_counted, counts
- Standardized method names in IVCollection: get_valid_counts,
get_valid_length, get_length, get_counts, et c
- IVCollection/Transcript openers/assemblers all return generators and can
take multiple input files
- IVCollection/Transcript openers/assemblers return lexically-sorted objects
- Update to GFF3 escaping conventions rather than URL escaping. Also applied
to GTF2 files
- Refactors to `cs` script, plus garbage collection to reduce memory usage
Added
.....
- Changelog
- Implementation of test suites
- Lazy assembly of GFF3 and GTF2 files to save memory in
`GTF2_TranscriptAssembler` and `GFF3_TranscriptAssembler`
- BigBed support, creation of BigBedReader and BigBedGenomeHash. AutoSQL
support
- Supported for truncated BED formats
- P-site offset script
- `get_count_vectors` script
- `counts_in_region` script
- UniqueFifo class
- Decorators: `parallelize, suppress_stderr, in_separate_process`
- variableStep export for `BAMGenomeArray`
- Support of GTF2 "frame" attribute for CDS features
Fixed
.....
- Bugfixes in minus strand offsets in crossmaps
- Fixed bug where minus strand crossmap features were ignored
- Bugfixes in CDS end export from Transcript when CDSes ended at the endpoint
of internal but not terminal introns on plus-strand transcripts
Deprecated
..........
- spliced_count_files
- Ingolia file tagalign import
- Deprecation of `GTF2_to_Transcripts` and `GFF3_to_Transcripts`