[Bioperl-l] pir format for input and output os sequences

[Heikki Lehvaslaiho]

Luisa,

The desc() method is implemented in Bio::PrimarySeq class and is used via 
inheritance by all other sequence classes.

It is populated by strings from SWISS-PROT DE line, GenProt DEFINITION line, 
and like.

Before writing out the pir format you can set:

$seq->desc('any useful information');

Hope this helps,

			-Heikki


On Thursday 13 May 2004 13:32, luisa pugliese wrote:
> Hi Bioperlers,
>     I am interessed at working with the pir format because it is widely
> used in homology modeling.
> I saw that among bioperl SeqIO methods there is also pir and that the print
> section of this method is:
>
> return unless $self->_print(">P1;".$seq->id(),
>         "\n", $seq->desc(), "\n",
>         $str, "*\n");
>
> In the second line the method would write:
>
> $seq->desc().
>
> I would like to fill this line with proper informations, but I didn't find
> the description of the desc method .
> Does anybody knows where can I find it or how can I pass some informations
> to it?
> Best regards
> Luisa
> =============================
> Luisa Pugliese, Ph.D.
> luisa.pugliese at safan-bioinformatics.it
> S.A.F.AN. BIOINFORMATICS
> Corso Tazzoli 215/13 -10137 Torino - ITALY
> tel +39 011 3026230
> cell. +39 333 6130644
>
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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