[Debian-med-packaging] Fwd: Re: Feature Suggestion with Patch - Please Advise

[Laszlo Kajan]

Dear Team, Charles, Erik, Steffen!

I need the hmmer3 functionality I describe below in point 1 and 3, and Sean Eddy (author/upstream of method) says there might be something like
this in version 3.1 (I am forwarding his email below).

But I need the functionality already, as is implemented in my patches.

* What do you recommend I do?:

1: I can patch hmmer3 and put it into our in-house repository at <http://rostlab.org/debian/>. People interested can grab it from there.

2: I can open a branch for hmmer3 in the DebMed repo, where I can commit my patches, and those who are interested can build it. We could put it
into 'experimental'. This option works together with 1.

3: I can patch hmmer3, mark these features as volatile/experimental wherever they are documented, with a note about Sean's intentions, and we
can upload it into Debian as a new version. This way others may benefit from my patches most easily. However, those who start relying on the new
features (and command line arguments) provided, will be upset (regardless of the warning) when the new command line arguments disappear. That is
in case Sean brings out these features under other arguments, or with somewhat different meaning, or not at all (yet).

So please advise. 1: is my default option in case of a timeout.

Thank you!

Best regards,

Laszlo

-------- Original Message --------
Subject: Re: Feature Suggestion with Patch
Date: Sat, 13 Oct 2012 21:39:26 +0000
From: Eddy, Sean <eddys at janelia.hhmi.org>
To: Laszlo Kajan <lkajan at rostlab.org>
CC: ~JF hmmer <~hmmer at janelia.hhmi.org>

Hi Laszlo,

Thanks, those look like sensible patches. These things have been on our to-do list. I'm in the middle of assembling the 3.1 release right now,
but I've put your patches in a safe place where I can come back to them when I get 3.1 further along, and I'll implement either your patches
exactly, or something similar. Thanks for sending them!

Sean


On Oct 12, 2012, at 7:13 PM, Laszlo Kajan wrote:

> Dear Sean!
> 
> I am Laszlo Kajan from Burkhard Rost's lab, bioinformatician, Debian maintainer.
> 
> I would like to use jackhmmer to search a smaller database to build up an HMM, and then search a bigger database with this model. The present
> version of jackhmmer (that I know of, 3.0-4 in Debian) does not support this fully, because:
> 
> 1: jackhmmer can not be started from a query /and/ a model, so I can not use the checkpoint model to restart it on the big database.
> 
> 2: hmmsearch can not be started from a model /and/ a query, so that it would produce an alignment including the query as jackhmmer does; it also
> can not do iterative search.
> 
> 3: jackhmmer saves the checkpoint HMM /before/ doing another iteration, therefore in order to get the checkpoint for 3 iterations I have to run
> actually 4. I would like to save those clock cycles.
> 
> I have prepared patches that solve 1 and 3 and allow me to search the big database with a model built on the smaller one, using jackhmmer
> (patches attached, series: jackhmmer_chkhmmstop, jackhmmer_restartfromhmm, jackhmmer_stop_restart_test). The results obtained from the restarted
> search are identical to a non-restart, when performed on the same database, i.e. 3 iterations on a database give the same results as one
> iteration starting from a checkpoint HMM saved before the 3rd iteration. This make me hope that my patches - though I do not have much knowledge
> about the internals of hmmer3 - are on the right path.
> 
> * Please comment on my patches and let me know if my approach is all right.
> 
> * Please consider adding the features (1 and 3) to hmmer in your next release.
> 
>  If you do approve my patches (or something with similar results), then I would like to include them in the Debian release of hmmer3. However
> this should only be a temporary solution, until your next release.
> 
> Please treat my feature suggestion and patches as a sign of my great appreciation of hmmer3. Thank you for releasing hmmer3 under a free
> software license.
> 
> Best regards,
> 
> Laszlo Kajan
> Rost Lab
> Debian Maintainer
> <jackhmmer_chkhmmstop.txt><jackhmmer_restartfromhmm.txt><jackhmmer_stop_restart_test.txt>