Your message dated Wed, 07 Dec 2022 18:00:14 +0000
with message-id <e1p2yim-001iee...@fasolo.debian.org>
and subject line Bug#1024465: fixed in pyfastx 0.8.4-1
has caused the Debian Bug report #1024465,
regarding ITP: pyfastx -- fast random access to sequences from FASTA/Q file
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1024465: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024465
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Étienne Mollier <emoll...@emlwks999.eu>
X-Debbugs-Cc: debian-de...@lists.debian.org
X-Debbugs-Cc: debian-...@lists.debian.org
* Package name : pyfastx
Version : 0.8.4
Upstream Author : Lianming Du
* URL : https://github.com/lmdu/pyfastx/
* License : Expat
Programming Lang: C, Python3
Description : fast random access to sequences from FASTA/Q file
The pyfastx is a lightweight Python C extension that enables users to randomly
access to sequences from plain and gzipped FASTA/Q files. This module aims to
provide simple APIs for users to extract sequence from FASTA and reads from
FASTQ by identifier and index number. The pyfastx will build indexes stored in
a sqlite3 database file for random access to avoid consuming excessive amount
of memory. In addition, the pyfastx can parse standard (sequence is spread
into multiple lines with same length) and nonstandard (sequence is spread into
one or more lines with different length) FASTA format.
.
It features:
.
* a single file for the Python extension;
* lightweight, memory efficient FASTA/Q file parsing;
* fast random access to sequences from gzipped FASTA/Q file;
* sequences reading from FASTA file line by line;
* N50 and L50 calculation of sequences in FASTA file;
* GC content and nucleotides composition calculation;
* reverse, complement and antisense sequences extraction;
* excellent compatibility: support for parsing nonstandard FASTA file;
* support for FASTQ quality score conversion;
* a command line interface for splitting FASTA/Q file.
This package is required for upgrading to augur 18.2.0. It will
be maintained in the Debian Med team. The packaging occurs in
the Debian Med group on Salsa[1].
[1]: https://salsa.debian.org/med-team/pyfastx
Have a nice day, :)
--
Étienne Mollier <emoll...@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/4, please excuse my verbosity.
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: pyfastx
Source-Version: 0.8.4-1
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
pyfastx, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1024...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated pyfastx package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 20 Nov 2022 16:58:50 +0100
Binary: pyfastx python3-pyfastx python3-pyfastx-dbgsym
Source: pyfastx
Architecture: amd64 source
Version: 0.8.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1024465
Description:
pyfastx - fast random access to sequences from FASTA/Q file - command
python3-pyfastx - fast random access to sequences from FASTA/Q file - python3
modul
Changes:
pyfastx (0.8.4-1) unstable; urgency=medium
.
* Initial release (Closes: #1024465)
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