Le jeu. 30 avr. 2015 à 17:42, Scott Kitterman <
debian@kitterman.com> a écrit :
On Thursday, April 30, 2015 05:13:03 PM Olivier Sallou wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Olivier Sallou <osallou@debian.org>
>
> * Package name : python-obitools
> Version : 1.1.16
> Upstream Author : Eric Coissac
> * URL : http://metabarcoding.org//obitools/
> * License : CeCILL-V2
> Programming Lang: Python
> Description : set of programs specifically designed for analyzing NGS
> data in a DNA metabarcoding contex
>
> The OBITools package is a set of programs specifically designed for
> analyzing NGS data in a DNA metabarcoding context, taking into account
> taxonomic information. OBITools enrich the Unix command line interface with
> a set of new commands dedicated to NGS data processing. Most of them have a
> name starting with the obi prefix. They automatically recognize the input
> file format amongst most of the standard sequence file formats (i.e. fasta,
> fastq, EMBL, and GenBank formats). Nevertheless, options are available to
> enforce some format specificity such as the encoding system used in fastq
> files for quality codes. Most of the basic Unix commands have their
> OBITools equivalent (e.g. obihead vs head, obitail vs tail, obigrep vs
> grep), which is convenient for scientists familiar with Unix. The main
> difference between any standard Unix command and its OBITools counterpart
> is that the treatment unit is no longer the text line but the sequence
> record. As a sequence record is more complex than a single text line, the
> OBITools programs have many supplementary options compared to their Unix
> equivalents.
According to the trove information on pypi [1] this is python only, not
python3. We were hoping to not increase the amount of python packages needing
porting to python3. Have you discussed python3 plans with upstream?
Nope, not yet. However, as I discussed with one guy of the team some time ago, I do not think there is any plan to go to python3.
This is an academic tool, and very often, they only focus on getting something working and base maintenance.
I understand the need to plan python3 switch, however we cannot block tools used by the community.
I will ask upstream anyway.
Scott K
[1] https://pypi.python.org/pypi/OBITools/1.1.16
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