[Bioperl-l] hmmer3/hmmscan parser

[Chris Fields]

On May 24, 2010, at 7:46 PM, Thomas Sharpton wrote:

> 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.

The commit doesn't show any added files.  The original code apparently is on a branch of bioperl-dev, though (think this was pointed out on IRC):

http://github.com/bioperl/bioperl-dev/tree/bioperl-hmmer3

Maybe that was the mixup?

> 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.

I started up a new github repo for it.  You would just need to let me know your github ID so I can add you to it.  Then (after you are added) the instructions are here:

http://github.com/bioperl/bioperl-hmmer3

> 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

No problem.  Thanks for letting us know.

chris

> 
>> 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 ...
>> 
>