Bug#856661: ITP: transit -- statistical calculations of essentiality of genes or genomic regions
On 03/03/2017 03:18 PM, Andreas Tille wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Andreas Tille <tille@debian.org>
>
> * Package name : transit
> Version : 2.0.2
> Upstream Author : Michael A. DeJesus, Chaitra Ambadipudi, and Thomas R. Ioerger
> * URL : http://pythonhosted.org/tnseq-transit/transit_overview.html
> * License : GPL
> Programming Lang: Python
> Description : statistical calculations of essentiality of genes or genomic regions
> This is a software that can be used to analyze Tn-Seq datasets. It
> includes various statistical calculations of essentiality of genes or
> genomic regions (including conditional essentiality between 2
> conditions). These methods were developed and tested as a collaboration
> between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M)
> .
> TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1
> or Tn5 datasets.
> .
> TRANSIT assumes you have already done pre-processing of raw sequencing
> files (.fastq) and extracted read counts into a .wig formatted file.
> The .wig file should contain the counts at all sites where an insertion
> could take place (including sites with no reads). For Himar1 datasets
> this is all TA sites in the genome. For Tn5 datasets this would be all
> nucleotides in the genome.
>
>
> Remark: This package will be maintained by the Debian Med team at
> https://anonscm.debian.org/cgit/debian-med/transit.git
Hi,
The package name from upstream (as per the setup.py) is called
"tnseq-transit" (see [1]). This looks a better package name to me than
just "transit" which feels like a network protocol package. How about
using tnseq-transit as a Debian package name then?
Hoping this is a good suggestion,
Cheers,
Thomas Goirand (zigo)
[1] https://github.com/mad-lab/transit/blob/master/setup.py#L28
Reply to: