Bio::SearchIO::infernal.pm

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Bio::SearchIO::infernal.pm

Ashton Trey Belew
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  Good evening,
  I was fiddling with cmsearch this evening and discovered that the
current infernal parser does not play well with the new version (1.1)
of infernal.  I am currently hacking on the function parse_latest() in
an attempt to handle the differences in formats but have hit a bit of
a wall in picking up the accessions and descriptions from the cmsearch
output.
  In a peculiar turn of events, if parse_latest does not find the
accession/description fields, it seems to repeat the PARSER: loop
indefinitely, in my case repeating $self->_readline on the the 10th hit.

  I will keep poking at it this evening, but if anyone has made
greater headway, I would love some pointers.

  Thank you for your time,
 -Trey
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Re: Bio::SearchIO::infernal.pm

Fields, Christopher J
Let us know if you manage to get it working, we’ll be glad to accept a patch!

chris

On Jul 30, 2014, at 10:25 PM, Ashton Trey Belew <[hidden email]> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
>  Good evening,
>  I was fiddling with cmsearch this evening and discovered that the
> current infernal parser does not play well with the new version (1.1)
> of infernal.  I am currently hacking on the function parse_latest() in
> an attempt to handle the differences in formats but have hit a bit of
> a wall in picking up the accessions and descriptions from the cmsearch
> output.
>  In a peculiar turn of events, if parse_latest does not find the
> accession/description fields, it seems to repeat the PARSER: loop
> indefinitely, in my case repeating $self->_readline on the the 10th hit.
>
>  I will keep poking at it this evening, but if anyone has made
> greater headway, I would love some pointers.
>
>  Thank you for your time,
> -Trey
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1
>
> iD8DBQFT2bcsF9UIceSIYeoRArqPAKCR4ueCEKhamjkQzwHcyXWix9hy7QCgwaIf
> Icd5hZI3yARPRUpkcpHtZ2U=
> =brNJ
> -----END PGP SIGNATURE-----
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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