Skip to content

Commit

Permalink
Bump version and update readme.
Browse files Browse the repository at this point in the history
  • Loading branch information
mdshw5 committed Feb 13, 2015
1 parent e272eaf commit 9001030
Show file tree
Hide file tree
Showing 2 changed files with 4 additions and 90 deletions.
92 changes: 3 additions & 89 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -304,97 +304,11 @@ A lower-level Faidx class is also available:
- Start and end coordinates are 1-based.


Changes
Changelog
-------
*New in version 0.3.4*:

- `--delimiter` option for cli script and `split_char` argument for `Fasta` and `Faidx`

*New in version 0.3.3*:

- `--split-files` option writes each returned sequence to an individual file. Names are generated based on the sequence name and region coordinates.
- `--stats` option prints the name and sequence length for each entry, suitable for use as a UCSC-style [chrom.sizes](http://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes) file.
- Sequence `longname` attribute allows access to "chr:start-end (complement)" formatted names


*New in version 0.3.2*:

- Fasta `__getitem__` no longer initializes new FastaRecord classes
- Faidx `read_ahead` attribute implementaion avoids unnecessary disk hits (`#34 <https://github.com/mdshw5/pyfaidx/issues/34>`_)

*New in version 0.3.1*:

- Fasta can now accept an integer index in addition to string keys.

*New in version 0.3.0*:

- FastaRecord now works as a line-based iterator (`#30 <https://github.com/mdshw5/pyfaidx/issues/30>`_)
- Added MutableFastaRecord class that allows same-length in-place replacement for FASTA (`#29 <https://github.com/mdshw5/pyfaidx/issues/29>`_)

*New in version 0.2.9*:

- Added read-ahead buffer for fast sequential sequence access (`#26 <https://github.com/mdshw5/pyfaidx/issues/26>`_)
- Fixed a condition where `as_raw` parameter was not respected (`#27 <https://github.com/mdshw5/pyfaidx/issues/27>`_)

*New in version 0.2.8*:

- Small internal refactoring

*New in version 0.2.7*:

- Faidx and Fasta `strict_bounds` bounds checking logic is more correct
- Fasta `default-seq` parameter now works
- CLI script `faidx` now takes a BED file for fetching regions from a fasta

*New in version 0.2.6*:

- Faidx no longer has `raw_index` attribute or `rebuild_index` method (reduce memory footprint)
- Faidx index memory usage decreased by 31-40%
- .fai creation is streaming, performance increase for very large indices
- Possible speed regression when performing many small queries using `Fasta` class

*New in version 0.2.5*:

- Fasta and Faidx can take `default-seq` in addition to `as_raw`, `key_function`,
and `strict_bounds` parameters.
- Fixed issue `#20 <https://github.com/mdshw5/pyfaidx/issues/20>`_
- Faidx has attribute `raw_index` which is a list representing the fai file.
- Faidx has `rebuild_index` and `write_fai` functions for building and writing
`raw_index` to file.
- Extra test cases, and test cases against Biopython SeqIO

*New in version 0.2.4*:

- Faidx index order is stable and non-random

*New in version 0.2.3*:

- Fixed a bug affecting Python 2.6

*New in version 0.2.2*:

- `Fasta` can receive the `strict_bounds` argument

*New in version 0.2.1*:

- `FastaRecord` str attribute returns a string
- `Fasta` is now an iterator

*New in version 0.2.0*:

- `as_raw` keyword arg for `Faidx` and `Fasta` allows a simple string return type
- `__str__` method for `FastaRecord` returns entire contig sequence

*New in version 0.1.9*:

- line wrapping of ``faidx`` is set based on the wrapping of the indexed
fasta file
- added ``--reverse`` and ``--complement`` arguments to ``faidx``

*New in version 0.1.8*:

- ``key_function`` keyword argument to ``Fasta`` allows lookup based on function
output
Please see the `releases <https://github.com/mdshw5/pyfaidx/releases>`_ for a
comprehensive list of version changes.

Acknowledgements
----------------
Expand Down
2 changes: 1 addition & 1 deletion pyfaidx/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@

dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)')

__version__ = '0.3.4'
__version__ = '0.3.5'


class FastaIndexingError(Exception):
Expand Down

0 comments on commit 9001030

Please sign in to comment.