./biology/py-dnaio, Read and write FASTQ and FASTA files

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Branch: CURRENT, Version: 0.9.1, Package name: py310-dnaio-0.9.1, Maintainer: bacon

dnaio is a Python 3 library for fast input and output of FASTQ and FASTA files.
It supports paired-end data in separate files, interleaved paired-end in a
single file and compression using gzip, bzip, and xz.


Master sites:

Filesize: 40.619 KB

Version history: (Expand)


CVS history: (Expand)


   2022-11-14 11:39:40 by Thomas Klausner | Files touched by this commit (3) | Package updated
Log message:
py-dnaio: update to 0.9.1.

v0.9.1 (2022-08-01)
-------------------

* :pr:`85`: macOS wheels are now also built as part of the release procedure.
* :pr:`81`: API documentation improvements and minor code refactors for
  readability.

v0.9.0 (2022-05-17)
-------------------

* :pr:`79`: Added a `records_are_mates` function to be used for checking whether
  three or more records are mates of each other (by checking the ID).
* :pr:`74`, :pr:`68`: Made FASTQ parsing faster by implementing the check for
  ASCII using SSE vector instructions.
* :pr:`72`: Added a `tutorial \ 
<https://dnaio.readthedocs.io/en/latest/tutorial.html>`_.

v0.8.0 (2022-03-26)
-------------------

* Preliminary documentation is available at
  <https://dnaio.readthedocs.io/>.
* :pr:`53`: Renamed ``Sequence`` to `SequenceRecord`.
  The previous name is still available as an alias
  so that existing code will continue to work.
* When reading a FASTQ file, there is now a check that ensures that
  all characters are ASCII.
* Function ``record_names_match`` is deprecated, use `SequenceRecord.is_mate` \ 
instead.
* Dropped Python 3.6 support as it is end-of-life.

v0.7.1 (2022-01-26)
-------------------

* :pr:`34`: Fix parsing of FASTA files that just contain a comment and no reads

v0.7.0 (2022-01-17)
-------------------

* @rhpvorderman contributed many performance improvements in :pr:`15`,
  :pr:`17`, :pr:`18`, :pr:`20`, :pr:`21`, :pr:`22`, :pr:`23`. Reading
  and writing FASTQ files and reading of paired-end FASTQ files was
  sped up significantly. For example, reading uncompressed FASTQ is
  50% faster (!) than before.
* :pr:`28`: Windows support added

v0.6.0 (2021-09-28)
-------------------

* :pr:`12`: Improve FASTQ writing speed twofold (thanks to @rhpvorderman)

v0.5.2 (2021-09-07)
-------------------

* :issue:`7`: Ignore a trailing "3" in the read id
   2022-01-04 21:55:40 by Thomas Klausner | Files touched by this commit (1595)
Log message:
*: bump PKGREVISION for egg.mk users

They now have a tool dependency on py-setuptools instead of a DEPENDS
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73)
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73)
Log message:
biology: Remove SHA1 hashes for distfiles
   2021-05-23 01:24:17 by Nia Alarie | Files touched by this commit (1)
Log message:
py-dnaio: unbreak pkgsrc tree. revert removal of PYTHON_VERSIONS_INCOMPATIBLE.
   2021-05-21 13:38:13 by Adam Ciarcinski | Files touched by this commit (3) | Package updated
Log message:
py-dnaio: updated to 0.5.1

v0.5.1
Add py.typed and distribute .pyi files
   2021-04-22 10:38:59 by Nia Alarie | Files touched by this commit (1)
Log message:
py-dnaio: mark incompatible with python 2
   2021-03-04 14:06:34 by Makoto Fujiwara | Files touched by this commit (1)
Log message:
(biology/py-dnaio) +BUILD_DEPENDS+= py-setuptools_scm (other than 27 are fixed)