[Biopython] HMMER / Pfam support

[Ruchira Datta]

I had written a HMMER3 parser independently (i.e., not based on any previous
work), if that helps.  However, I wrote it thinking of our group's needs, so
it may not be BioPythonic.

--Ruchira

On Fri, Dec 3, 2010 at 5:22 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Dec 2, 2010 at 10:53 PM, Kyle <kellrott at gmail.com> wrote:
> > I would like to submit my hmmer branch for merge into the main BioPython
> > tree, targeting inclusion in 1.57.
> > This branch adds support for HMMER3 file parsing and some Pfam related
> file
> > work. It's adapted from the PfamScan perl code found at
> > ftp://ftp.sanger.ac.uk/pub/rdf/PfamScanBeta/
> > The code can be found at
> https://github.com/kellrott/biopython/tree/hmmer
> >
> > Kyle
>
> Hi Kyle,
>
> I've had a quick look at the HMMER bits (but not the PFAM stuff)
> and have some initial comments.
>
> I'm concerned about the apparent use of Jaina Mistry & John Tate's
> Perl code which is under the GPL v2+ and thus cannot be included
> in Biopython. If you basically copied their code and translated it into
> Python. I think to be safe you'll have to ask the origin authors'
> permission to re-license it for Biopython (MIT/BSD style). If your
> code is a fresh implementation using their approach you may be
> OK, but the module text should be clarified.
>
> Does hmmscan work on Windows? Would there be much point
> writing a Bio.Application style wrapper class for it, rather than or
> to be used within your Bio.hmmer.HMMScan function etc? A unit
> test for calling the tool would be good, e.g. test_hmmer_tool.py
> which can be made conditional on the tool being found.
>
> In Bio.hmmer you have two functions, parseHMMER3 and
> parseMultiHMMER3 taking file handles, used for a single
> record and multiple records (right?). It would match Biopython
> usage to call these read (single) and parse (iterator)
>
> Is there anything here for HMMER2? I saw some apparent
> stub entries in the code so I guess not.
>
> A minor thing: In your unit test file test_hmmer.py do you really
> need to use the obsolete string module? Can't you use a string
> method?
>
> Also since this is quite a long lived branch looking over your
> changes isn't so simple what with all the merges. I'd find it
> easier to review the changes if you could rebase it off the
> current master, e.g. assuming you cloned from *your*
> repository on github, and added the official one as remote
> name upstream, something like this should do it:
>
> git checkout hmmer
> git branch hmmer_dec2010
> git checkout hmmer_dec2010
> git fetch upsteam
> git rebase upstream/master
> git push origin hmmer_dec2010
>
> (Untested, but something like that).
>
> Is the PFAM stuff on this branch required for your HMMER
> code, or could we deal with the HMMER stuff  separately
> first? If so a "clean" new branch with just the HMMER
> stuff would be preferable (if it makes life easier, you
> could do it as a single commit - assuming you don't care
> about the history to date)
>
> Peter
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