[Bioperl-guts-l] [BioPerl - Bug #3264] (New) Bio::SearchIO::hmmer2 fails with Bio::Tools::Run::Hmmer, with diagnosis

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Thu Jul 14 19:03:05 EDT 2011


Issue #3264 has been reported by George Hartzell.

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Bug #3264: Bio::SearchIO::hmmer2 fails with Bio::Tools::Run::Hmmer, with diagnosis
https://redmine.open-bio.org/issues/3264

Author: George Hartzell
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


I'm working with clones of the git repository from this morning.

I can't get bioperl-run/t/Hmmer.t to pass.

Digging into it I believe that the root of the problem is that Bio::SearchIO:hmmer::new reads a couple of lines off of the filehandle in order to figure out the hmmer version and then assumes that it can use seek to rewind the input stream back to the beginning.

Unfortunately Bio::Tools::Run::Hmmer ends up passing in a filehandle that's reading off of a pipe.

Line 132 of Bio/SearchIO/hmmer.pm should become something like this:

            @seek($fh, 0, 0) or die "Unable to seek to start of input.";@

and then "someone" needs to figure out how to make the format guesser Do The Right Thing when it's input is a pipe.



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