[Bioperl-l] hmmer3/hmmscan parser

[Thomas Sharpton]

Hi all,

To clarify, I have constructed a SearchIO parser for hmmer3 hmmscan and
hmmsearch output. It appears to be fully functional and I have had a handful
of users test and integrate this module.

We decided to push this module into a standalone svn repo (bioperl-hmmer3).
I am a bit confused about why the repo is empty, as I committed the code
back in March and have made a few updates since then to correct bugs
identified by test users.  Perhaps I screwed something up during the last
commit.

Chris, should I just add the code to the github repo? I might need a pointer
on how to do this without screwing it up.

Kai, I can mail an archive of the parser your way if you're in a hurry. With
some assistance from Chris et. al., I expect the code to be in the github
repo by the day's end.

Apologies for any confusion and the delayed reply - I've been on the road.

Best,
Tom

On May 21, 2010 4:24 PM, "Chris Fields" <cjfields at illinois.edu> wrote:

To add to this, it appears there was an attempt to commit this code to SVN
just prior to the github migration, but nothing is present in the svn repo
(which is still reachable, but is read-only).  Empty repos were not migrated
over.  Thomas, let me know if you need addition to the github repo, would be
easy enough to add this in when ready.

Relevant commit msg here:

http://lists.open-bio.org/pipermail/bioperl-guts-l/2010-May/031172.html

perllib cjfields$ svn ls svn+ssh://
dev.open-bio.org/home/svn-repositories/bioperl
===========================================
dev.open-bio.org - Authorized Access Only
===========================================
...<snip irrelevant repos>
bioperl-hmmer3/
...<snip irrelevant repos>
perllib cjfields$ svn ls svn+ssh://
dev.open-bio.org/home/svn-repositories/bioperl/bioperl-hmmer3
===========================================
dev.open-bio.org - Authorized Access Only
===========================================
perllib cjfields$

chris


On May 21, 2010, at 4:56 PM, Kai Blin wrote:

> Hi list, hi Thomas,
>
> I've just bumped into the ...