[Bioperl-l] length of hit->description

Francisco J. Ossandón fossandonc at hotmail.com
Thu Jul 24 20:45:28 UTC 2014

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
.pm), which means that probably the "description" subroutine used is the one
from GenericHit module
=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

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:

But maybe it is just for blast and not fasta.

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