[Bioperl-l] hmmer3.pm question re query and hit coordinates

Kai Blin kai.blin at biotech.uni-tuebingen.de
Thu Jul 12 09:43:19 EDT 2012


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On 2012-07-11 23:25, Wibowo Arindrarto wrote:

Hi,

> The current Biopython parser for the plain text format parses the
> very first line to find out which HMMER flavor produces the result.
> Both 'hmm from' and 'hmmto' are query coordinates if the flavor is
> hmmsearch or phmmer; and they're hit coordinates if the flavor is
> hmmscan.

Whoops. I mostly looked at hmmscan when writing the parser, because
that's the file format I needed for my code. The code clearly should
follow the way the hmmer2 parser works, and differentiate between
hmmsearch and hmmscan type output.

As I said on the bug report, I'm happy to look at code fixing this.

> This information is not available in other HMMER command line
> output formats (tblout and domtblout), which as Peter has
> mentioned, required us to treat different flavors of the table
> output as different formats for the time being.

As far as I'm aware, BioPerl currently doesn't parse the table output
format.

Seeing how much repeated pain we run into with all these parsers in
the different Bio* projects, I wonder if there was a smarter way to
deal with parsing. Maybe at least some shared grammar file that we
could use for testing, to make sure we at least have the same
expectations about file formats in the different language
implementations. Ideally we'd auto-generate the parsers from the
grammar specification, but I guess that'll stay wishful thinking for
quite a bit.

> Fortunately, after contacting the HMMER developers they mentioned
> that this is not the case anymore in their development branch (and
> their future planned release).

That's certainly good news. :)

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben


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