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

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Branch: CURRENT, Version: 1.2.0, Package name: py311-dnaio-1.2.0, Maintainer: pkgsrc-users

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: 56.86 KB

Version history: (Expand)

CVS history: (Expand)


   2024-04-11 01:48:52 by Jason Bacon | Files touched by this commit (1) 
Log message:
biology/py-dnaio: Release to pkgsrc-users@

dnaio is used only by cutadapt, which has been replaced by
fastq-trim in my toolbox
   2024-02-15 22:45:02 by Thomas Klausner | Files touched by this commit (1) 
Log message:
py-dnaio: add missing tool
   2024-02-10 14:07:54 by Jason Bacon | Files touched by this commit (4) 
Log message:
biology/py-dnaio: Update to 1.2.0

Numerous bug fixes and enhancements since 0.9.1
Changes: https://github.com/marcelm/dnaio/tags
   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.