[Biopython] Support for HHSearch output form in Biopython SearchIO module

[Thomas, Jens]

Hi Bow,

I was worried someone was going to say that... ;)

Ok, I'll start looking into this and submit a pull request when I've got something working.

Best wishes,

Jens
________________________________________
From: Wibowo Arindrarto <w.arindrarto at gmail.com>
Sent: 01 February 2019 12:46:50
To: Thomas, Jens
Cc: biopython at mailman.open-bio.org
Subject: Re: [Biopython] Support for HHSearch output form in Biopython SearchIO module

Hi Jens,

There are no plans to do that at the moment. If you are interested in
having this feature (and if the output does fit the SearchIO model),
you are welcome to write a pull request for it and I'd be happy to do
the review.

One of the things that need be done is to generate the possible ways
the file format may look like, especially since it does not seem to be
a standard file format like JSON or XML. This can be quite cumbersome,
but again, if you are interested and you already have some outputs
lying around, that would be a good start. Most useful would be to
cover the general cases (what a normal, relatively speaking, output
looks like) and some of the edge cases (e.g. what does an empty result
look like, can a single hit contain multiple alignments, etc.). Then,
we can start writing the actual parsers.

Cheers,
Bow

On Fri, Feb 1, 2019 at 1:26 PM Thomas, Jens <Jens.Thomas at liverpool.ac.uk> wrote:
>
> Hello,
>
> Are there any plans to support the .hhr output format in Biopython, so that it would be possible to use the results of HHBlits or HHSearch sequence searches?
>
> Best wishes,
>
> Jens
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