Releases | Open Source Science

What's Changed

Keep first empty bgzf block in index. Add tests, closes #238 by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/239

This release fixes a bug in the new BGZF indexing strategy. Anyone using v0.9.0-v0.9.0.2 should upgrade. Thanks @chtsai0105!

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.9.0.2...v0.9.0.3

- Python
Published by mdshw5 6 months ago

What's Changed

Add test case for issue described in #228 by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/233
Work on test coverage by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/234
Add tests for FastaVariant and sequence masking by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/235
feat: Add long name support for bgzf files by @ggydush in https://github.com/mdshw5/pyfaidx/pull/237

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.9.0.1...v0.9.0.2

- Python
Published by mdshw5 6 months ago

What's Changed

feat: Add bgzip index support for fsspec objects by @ggydush in https://github.com/mdshw5/pyfaidx/pull/232

New Contributors

@ggydush made their first contribution in https://github.com/mdshw5/pyfaidx/pull/232

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.9.0...v0.9.0.1

- Python
Published by mdshw5 6 months ago

What's Changed

Detect and preserve original line terminator characters (closes #170) by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/227
Update test data and tests fixes #230 by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/231
Support for constructing and using GZI format files for BGZF compressed FASTA by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/164

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.8.2...v0.9.0

- Python
Published by mdshw5 6 months ago

What's Changed

fix: check for file before closing in exit by @kdm9 in https://github.com/mdshw5/pyfaidx/pull/229

New Contributors

@kdm9 made their first contribution in https://github.com/mdshw5/pyfaidx/pull/229

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.8.1.4...v0.8.2

- Python
Published by mdshw5 6 months ago

What's Changed

Remove Depsy from README by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/225
do not needlessly require importlib_metadata by @a-detiste in https://github.com/mdshw5/pyfaidx/pull/226

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.8.1.3...v0.8.1.4

- Python
Published by mdshw5 10 months ago

What's Changed

remove setuptools from runtime dependencies by @emollier in https://github.com/mdshw5/pyfaidx/pull/224

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.8.1.2...v0.8.1.3

- Python
Published by mdshw5 over 1 year ago

What's Changed

Update documentation for get_seq which uses 1-based closed intervals by @eroller in https://github.com/mdshw5/pyfaidx/pull/222
Add packaging library for #220 by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/223

New Contributors

@eroller made their first contribution in https://github.com/mdshw5/pyfaidx/pull/222

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.8.1.1...v0.8.1.2

- Python
Published by mdshw5 over 1 year ago

pyfaidx - v0.8.1.1

This is a minor correction to the bgzip example from #216. Thanks @jmarshall!

- Python
Published by mdshw5 about 2 years ago

What's Changed

Better message about bgzip compression errors: Update init.py by @rraadd88 in https://github.com/mdshw5/pyfaidx/pull/216

New Contributors

@rraadd88 made their first contribution in https://github.com/mdshw5/pyfaidx/pull/216

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.8.0...v0.8.1

- Python
Published by mdshw5 about 2 years ago

What's Changed

remove old Python 2 hybridation by @a-detiste in https://github.com/mdshw5/pyfaidx/pull/215
This release drops support for Python 2. If you need to use this module with a Python 2 interpreter, please use a version from 0.7 or earlier!

New Contributors

@a-detiste made their first contribution in https://github.com/mdshw5/pyfaidx/pull/215

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.7.2.2...v0.8.0

- Python
Published by mdshw5 about 2 years ago

What's Changed

Update codecov action by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/210
Replace usage of pkg_resources API by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/213

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.7.2.1...v0.7.2.2

- Python
Published by mdshw5 over 2 years ago

What's Changed

missing setuptools dependency in v0.7.2 by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/207

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.7.2...v0.7.2.1

- Python
Published by mdshw5 about 3 years ago

What's Changed

Add use case for indexing FASTA with suppressed output by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/198
Update python versions in CI by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/197
fix bgzf test failure with biopython 1.80 by @emollier in https://github.com/mdshw5/pyfaidx/pull/199
Switch to pyproject.toml by @marcelm in https://github.com/mdshw5/pyfaidx/pull/200
fix ResourceWarning: unclosed file by @siebrenf in https://github.com/mdshw5/pyfaidx/pull/202
Move the --invert-match example to the top by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/204
'Sequence.gc' Method for IUPAC bases by @Bardia-Masudy in https://github.com/mdshw5/pyfaidx/pull/205

New Contributors

@emollier made their first contribution in https://github.com/mdshw5/pyfaidx/pull/199
@siebrenf made their first contribution in https://github.com/mdshw5/pyfaidx/pull/202
@Bardia-Masudy made their first contribution in https://github.com/mdshw5/pyfaidx/pull/205

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.7.1...v0.7.2

- Python
Published by mdshw5 about 3 years ago

What's Changed

pathlib.Path can be passed to Fasta and Faidx by @palao in https://github.com/mdshw5/pyfaidx/pull/184
Bump minimum python to 3.7 by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/195
fix: remove seemingly superfluous import of pysam by @johanneskoester in https://github.com/mdshw5/pyfaidx/pull/194
Merge changes from #184 to release by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/196

New Contributors

@palao made their first contribution in https://github.com/mdshw5/pyfaidx/pull/184
@johanneskoester made their first contribution in https://github.com/mdshw5/pyfaidx/pull/194

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.7.0...v0.7.1

- Python
Published by mdshw5 over 3 years ago

What's Changed

Add acidbio/bed tests by @mdshw5 in https://github.com/mdshw5/pyfaidx/pull/188
Minor change in pytest xfail usage in tests by @ap-- in https://github.com/mdshw5/pyfaidx/pull/191
Add fsspec support by @ap-- in https://github.com/mdshw5/pyfaidx/pull/190
Implement fsspec handling for indexname by @ap-- in https://github.com/mdshw5/pyfaidx/pull/193

New Contributors

@ap-- made their first contribution in https://github.com/mdshw5/pyfaidx/pull/191

Full Changelog: https://github.com/mdshw5/pyfaidx/compare/v0.6.4...v0.7.0

- Python
Published by mdshw5 over 3 years ago

pyfaidx - v0.6.4

Migrated test suite from nose to pytest
Removed some deprecated function calls (#185)
Added support for pathlib.Path (#184)

- Python
Published by mdshw5 about 4 years ago

pyfaidx - v0.6.3.1

Removes large test data accidentally added in last release

- Python
Published by mdshw5 over 4 years ago

pyfaidx - v0.6.3

FastaVariant raises an exception when the requested sequence is not present in both the FASTA and VCF file (#180) (Thanks @lldelisle!)

- Python
Published by mdshw5 over 4 years ago

pyfaidx - v0.6.2

Fixed reverse and complement cli parameters to also work with sequence transformation (#178)

- Python
Published by mdshw5 over 4 years ago

pyfaidx - v0.6.1

Add better documentation in help text #177

- Python
Published by mdshw5 over 4 years ago

pyfaidx - v0.6.0

Make index creation atomic #174 (thanks @marco-mariotti)

- Python
Published by mdshw5 over 4 years ago

pyfaidx - v0.5.9.5

This is a small bug fix for #172, and allows proper counting of all IUPAC bases when using faidx --transform nucleotide.

- Python
Published by mdshw5 almost 5 years ago

pyfaidx - v0.5.9.2

This release fixes a bug encountered when retrieving sequence from FASTA files with "Windows" line endings ("/r/n") #141. Thanks @andrewhill157. There is no need to re-index files.

- Python
Published by mdshw5 about 5 years ago

pyfaidx - v0.5.9.1

Refactored FAI writing to account for system locale setting (#166) @folded

- Python
Published by mdshw5 over 5 years ago

pyfaidx - v0.5.9

more efficient iterator method for Fasta objects in #163 (thanks @C-nit)

- Python
Published by mdshw5 over 5 years ago

pyfaidx - v0.5.8

Implemented Fasta.__len__ (#157)
Sequence instances can now be compared against strings (#158 thanks @Maarten-vd-Sande)

- Python
Published by mdshw5 about 6 years ago

pyfaidx - v0.5.7

Fasta instances now have dictionary methods: Fasta.keys returns sequence names, Fasta.values returns FastaRecord instances, and Fasta.items returns a tuple of (key, value) pairs. #156 (thanks @Maarten-vd-Sande)

- Python
Published by mdshw5 about 6 years ago

pyfaidx - v0.5.6

Support for returning zero-length sequences (#155 and #93 see example below) (thanks @prihoda!)

```

from pyfaidx import Fasta fasta = Fasta('data/genes.fasta', strict_bounds=True) len(fasta['gi|557361099|gb|KF435150.1|'][100:100] == 0 True ```

- Python
Published by mdshw5 about 6 years ago

pyfaidx - v0.5.5.2

minor bug fix release adding support for python 3.7 (#145)

- Python
Published by mdshw5 over 7 years ago

pyfaidx - v0.5.5.1

Added better exceptions for files that do not contain any valid sequences (#144)

- Python
Published by mdshw5 over 7 years ago

pyfaidx - v0.5.5

Added proper BGZF support, fixing #131. Note: this fix requires code present in Biopython 1.73, which is not yet released. If you need this functionality in the mean time, install the biopython development version
Enhancement to faidx script: allow -v to be specified alongside -g (#142). Thanks @daler!

- Python
Published by mdshw5 over 7 years ago

pyfaidx - v0.5.4.2

Fixes #141, adding support for FASTA files containing carriage returns (Windows formatted files)

- Python
Published by mdshw5 over 7 years ago

pyfaidx - v0.5.4.1

Fixes #140 by changing the --default-seq argument in the faidx script to default to None

- Python
Published by mdshw5 over 7 years ago

pyfaidx - v0.5.4

This release adds a numpy array interface for FastaRecord objects (see #139).

- Python
Published by mdshw5 almost 8 years ago

pyfaidx - v0.5.3.1

This is a bug fix release to properly support changes in #134 and PR in #138.

- Python
Published by mdshw5 about 8 years ago

pyfaidx - v0.5.3

Added build_index argument for Faidx and Fasta (#134)
Raise IndexNotFoundError and FastaNotFoundError instead of IOError when files aren't readable (#134)

- Python
Published by mdshw5 about 8 years ago

pyfaidx - v0.5.2

Fixes an issue with faidx --transform bed which used [1, 1] coordinates and now uses (0, 1] coordinates as specified by BED

- Python
Published by mdshw5 about 8 years ago

pyfaidx - v0.5.1

Spliced sequence retrieval #127 (Thanks @simonvh)

- Python
Published by mdshw5 over 8 years ago

pyfaidx - v0.5.0.1

Removed BGZF warning (#123) since the test suite contains good coverage of this feature.

- Python
Published by mdshw5 over 8 years ago

pyfaidx - v0.5.0

coordinates with start > end can be auto reverse complemented using --auto-strand argument (#120)
--no-coords flag in faidx script suppresses "sequence:start-end" in output sequence headers (#121)
Sequence.long_name is deprecated in favor of Sequence.fancy_name. Sequence.longname() is now removed from the codebase after previous DeprecationWarnings.

- Python
Published by mdshw5 over 8 years ago

pyfaidx - v0.4.9.2

Fixed issue in key_function validation logic

- Python
Published by mdshw5 over 8 years ago

pyfaidx - v0.4.9.1

Faster faidx -i nucleotide code

- Python
Published by mdshw5 over 8 years ago

pyfaidx - v0.4.9

Support for resolving duplicate keys using duplicate_action argument to Fasta
Support for BGZF (block gzip compressed) FASTA files (#77) (Thanks @terrycojones!)
Support for numpy 32bit and 64bit integer comparisons (#114)
Better file locking and buffer flushing (#110)

- Python
Published by mdshw5 over 8 years ago

pyfaidx - v0.4.8.5

support for numpy integer types (#114)
key_function now applies to indexing as well as sequence retrieval (#111)
preliminary support for BGZF compressed files (#77) (Thanks @terrycojones)

- Python
Published by mdshw5 almost 9 years ago

pyfaidx - v0.4.8.4

Fasta(mutable = True) now performs synchronous writes (#110)

- Python
Published by mdshw5 almost 9 years ago

pyfaidx - v0.4.8.3

Sequence.longname is now Sequence.long_name to match FastaRecord.long_name (thanks @michaelbarton)
Sequence.longname now raises a DeprecationWarning, and will be eliminated in a future release.

- Python
Published by mdshw5 almost 9 years ago

pyfaidx - v0.4.8.2

Added faidx -e option.

- Python
Published by mdshw5 almost 9 years ago

pyfaidx - v0.4.8.1

Fixed unicode handling in Readme (#105)

- Python
Published by mdshw5 over 9 years ago

pyfaidx - v0.4.8

Includes better locking around index creation (#94, #96)
Fixed unicode encoding issue in setup.py (#104, #101)

- Python
Published by mdshw5 over 9 years ago

pyfaidx - v0.4.7.1

Fixes #79 and #80 (thanks @handstad) caused Sequence.end coordinates to be severely wrong.

- Python
Published by mdshw5 about 10 years ago

pyfaidx - v0.4.7

Fixes indexing for files containing blank lines between records (#83). Thanks @endrebak!

- Python
Published by mdshw5 about 10 years ago

pyfaidx - v0.4.6

Fixes Sequence.complement method with a more efficient implementation (#81) (@timodonnell)

- Python
Published by mdshw5 about 10 years ago

pyfaidx - v0.4.5.2

- Python
Published by mdshw5 over 10 years ago

pyfaidx - v0.4.5.1

Clarified license for inclusion in debian (@tillea)
Point release for #78

- Python
Published by mdshw5 over 10 years ago

pyfaidx - v0.4.4

Added --size-range option (#70)
Added --invert-match option

- Python
Published by mdshw5 over 10 years ago

pyfaidx - v0.4.3.1

Fixes a debugging statement I accidentally left in for release (#76)

- Python
Published by mdshw5 over 10 years ago

pyfaidx - v0.4.3

Fixes .complement naming behavior (#73)
Fixes Sequence.start and Sequence.end behavior (#74)
New case for raising a FastaIndexingError (#75)

- Python
Published by mdshw5 over 10 years ago

pyfaidx - v0.4.2

Adds support for returning uppercase sequence always (#71)

- Python
Published by mdshw5 over 10 years ago

pyfaidx - v0.4.1.1

faidx no longer exits when a sequence is not found. Instead a warning is produced. (#65)
fai index is not created if the modification time == fasta file (#66)

- Python
Published by mdshw5 almost 11 years ago

pyfaidx - v0.4.0.1

Fixed a bug involving whitespace in the .fai index file (#64)
Added more pygr compatibility (#21)
Documented FastaVariant class
Added --transform argument for faidx script (#58)
fai index is not created if the modification time == fasta file (#66)

- Python
Published by mdshw5 almost 11 years ago

pyfaidx - v0.3.9.1

New FastaVariant class for generating consensus sequences from a FASTA and taxi indexed VCF file (#59)
Fixed a bug in the index loading code (#62) (thanks @AlSimonsJax)
fai index is not created if the modification time == fasta file (#66)

- Python
Published by mdshw5 almost 11 years ago

pyfaidx - v0.3.8.1

--regex option for faidx script allows matching only certain records (#55)
filt_function argument for Faidx and Fasta allows filtering certain records based on a matching function (@jsilter)
fixed a bug (#56) when calling FastaRecord.long_name when using filt_function or split_char.
fai index is not created if the modification time == fasta file (#66)

- Python
Published by mdshw5 almost 11 years ago

pyfaidx - v0.3.7.1

Zero-length slices return an empty string (#53 thanks @vejnar)
Added FastaRecord.long_name property to extract the actual defline for a sequence from the file. (#54)
fai index is not created if the modification time == fasta file (#66)

- Python
Published by mdshw5 almost 11 years ago

pyfaidx - v0.3.6.1

Files with modification times newer than their indices are re-indexed (#50 - thanks @deannachurch)
Test data is now downloaded from NCBI using biopython, and unit tests are more independent (#51)
fai index is not created if the modification time == fasta file (#66)

- Python
Published by mdshw5 almost 11 years ago

New in version 0.3.5: - Fixes bug number #47, which did not allow sequences containing a lowercase "n" to be complemented (thanks @pschaughency) - Implements better error handling in #48 for sequences with invalid characters. - Added --version flag to faidx script (#42) - Now only allow integer values for read_ahead (#41)