[Bioperl-l] 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 <abelew at gmail.com> wrote:

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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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