[Bioperl-l] length of hit->description

[Francisco J. Ossandón]

For what I can see in that page, is the documentation of version 1.2, which
is really really old. Current BlasttHit module does not contain that
subroutine anymore
(https://github.com/bioperl/bioperl-live/blob/master/Bio/Search/Hit/BlastHit
.pm), which means that probably the "description" subroutine used is the one
from GenericHit module
(https://github.com/bioperl/bioperl-live/blob/master/Bio/Search/Hit/GenericH
it.pm):
=head2 description
Title : description
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args : [optional] scalar string to set the descrition
=cut

So if you are using an updated version, "->description(500)" is replacing
the description instead of doing what you expect. What BioPerl version are
you using??


-----Mensaje original-----
De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org
[mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] En
nombre de Antony03
Enviado el: jueves, 24 de julio de 2014 15:08
Para: Bioperl-l at mailman.open-bio.org
Asunto: Re: [Bioperl-l] length of hit->description

In fact, for the '500' it is because of this:

 Usage     : $hit_object->description( [integer] );
 Purpose   : Set/Get a description string for the hit.
             This is parsed out of the "Query=" line as everything after 
             the first chunk of non-whitespace text. Use $hit->name()
             to get the first chunk (the ID of the sequence).
 Example   : $description = $hit->description;
           : $desc_60char = $hit->description(60);  Argument  : Integer
(optional) indicating the desired length of the
           : description string to be returned.
 Returns   : String consisting of the hit's description or undef if not set.

That you can found here:
http://doc.bioperl.org/releases/bioperl-1.2/Bio/Search/Hit/BlastHit.html

But maybe it is just for blast and not fasta.



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