[Debian-med-packaging] Packaging pyfaidx instead of pyfasta [bpederse at gmail.com: Re: Test failures with pyfasta]

[Andreas Tille]

retitle 801721 ITP: python-pyfaidx - efficient pythonic random access to fasta subsequences
thanks

Hi,

while I initially intended to package pyfasta I realised that the unit
tests do not successfully pass.  When informing the author he
recommended to rather use pyfaidx and thus I simply turn this ITP into
one for pyfaidx.  I'll leave the packaging for pyfasta in SVN at the
said place and drop a note about the test suite issue.

Here are the metadata for the new ITP:

* Package name    : python-pyfaidx
  Version         : 0.4.2
  Upstream Author : Matthew Shirley <mdshw5 at gmail.com>
* URL             : https://github.com/mdshw5/pyfaidx
* License         : BSD-3
  Programming Lang: Python
  Description     : efficient pythonic random access to fasta subsequences
 Samtools provides a function "faidx" (FAsta InDeX), which creates a
 small flat index file ".fai" allowing for fast random access to any
 subsequence in the indexed FASTA file, while loading a minimal amount of
 the file in to memory. This python module implements pure Python classes
 for indexing, retrieval, and in-place modification of FASTA files using
 a samtools compatible index. The pyfaidx module is API compatible with
 the pygr seqdb module. A command-line script "faidx" is installed
 alongside the pyfaidx module, and facilitates complex manipulation of
 FASTA files without any programming knowledge.


As per pyfasta this package will also be maintained by the Debian Med
team in SVN
   svn://anonscm.debian.org/debian-med/trunk/packages/python-pyfaidx/trunk/


----- Forwarded message from Brent Pedersen <bpederse at gmail.com> -----

Date: Wed, 14 Oct 2015 15:04:31 -0600
From: Brent Pedersen <bpederse at gmail.com>
To: Andreas Tille <andreas at an3as.eu>
Subject: Re: Test failures with pyfasta

hmm, that's not good. but still, I recommend to use pyfaidx as I'm no
longer working on pyfaidx.

On Wed, Oct 14, 2015 at 2:53 PM, Andreas Tille <andreas at an3as.eu> wrote:
> Hi Brent,
>
> I intend to package pyfasta for the Debian distribution.  I tried to also
> run the unit tests:
>
>
> $ LC_ALL=C python setup.py nosetests
> running nosetests
> running egg_info
> writing pyfasta.egg-info/PKG-INFO
> writing top-level names to pyfasta.egg-info/top_level.txt
> writing dependency_links to pyfasta.egg-info/dependency_links.txt
> writing entry points to pyfasta.egg-info/entry_points.txt
> reading manifest file 'pyfasta.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> writing manifest file 'pyfasta.egg-info/SOURCES.txt'
> FF..creating new files:
> some.split.fasta
> creating new files:
> some.0.fasta
> some.1.fasta
> creating new files:
> some.0
> some.1
> creating new files:
> some.0.1Kmer.fasta
> some.1.1Kmer.fasta
> creating new files:
> some.0.10Kmer.2Koverlap.fasta
> some.1.10Kmer.2Koverlap.fasta
> creating new files:
> some.split.100Kmer.2Koverlap.fasta
> ...................................................Getötet
>
>
>
> The dots '.' come quite fast and than the output stops.  After several
> minutes (>10min) the computer slows down all processes and finally the
> kernel seems to kill the process (Getötet == killed).  Seems there is
> some infinite loop somewhere or so.
>
> Do you have any idea how to debug this issue or what information should
> be provided to track down the issue?
>
> Kind regards
>
>        Andreas.
>
> --
> http://fam-tille.de


----- End forwarded message -----

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