[Bioperl-l] ID line parsing in swiss.pm

[Allen Day]

There is some ID tag parsing in Bio::Tools::SwissProtParser that you can
use.  It should merged into swiss.pm, but I haven't done it yet.

-Allen

> Hi,
>
> The STANDARD/PRELIMINARY tag in SWISS-PROT (ID line) entries does not seem
> to be parsed by swiss.pm. This is quite useful to know if the entry is a
> SWISS-PROT or and sptrembl entry.
> This could be stored in the annotation object, something called like
> entry_tag.
>
>
>
> $line =~ /^ID\s+([^\s_]+)(_([^\s_]+))?\s+([^\s;]+);\s+([^\s;]+);/
>      || $self->throw("swissprot stream with no ID. Not swissprot in my
> book");
>    if( $3 ) {
>        $name = "$1$2";
>        $seq->division($3);
>    } else {
>        $name = $1;
>        $seq->division('UNK');
>    }
>
> ##################
> #Get here the entry tag
>  $seq->annotation->add_Annotation('entry_tag',$4);
> ##################
>
>    $seq->primary_id($1);
>    $seq->alphabet('protein');
>     # this is important to have the id for display in e.g. FTHelper,
> otherwise
>     # you won't know which entry caused an error
>    $seq->display_id($name);
>
>
> Any comments?
>
> Emmanuel
>
>
> -----------------------------------------------------
> Emmanuel Mongin mongin@ebi.ac.uk
> Tel:        +44 (0)1223 49 46 87
> Mobile:	    +44 (0)7813 32 12 82
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>
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