Bug#783833: ITP: python-obitools -- set of programs specifically designed for analyzing NGS data in a DNA metabarcoding contex
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?
Scott K
[1] https://pypi.python.org/pypi/OBITools/1.1.16
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