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

[Peter Cock]

On Wed, Jul 11, 2012 at 8:02 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Peng,
>
> Has this been filed as a bug yet?
>
>     https://redmine.open-bio.org/projects/bioperl
>
> Seems like it would be fairly easy to fix, but I want to track it just in case.
>
> chris

Hi all,

This could be the unfortunate fact that hmmscan and
hmmsearch return very similar tabular output, but
with query and hit interchanged. i.e. You need some
extra information to know which way round they are
(not possible with the current output). This was an
issue in Bow's Biopython SearchIO project - which
for the moment he solved by handling this as two
hmmer file formats. In the medium term we're hoping
hmmer3 will add some header information or something.

Peter