[Bioperl-l] accessing optional qualifiers within features?

[Samuel Aparicio]

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Hi - Thanks for this, the example makes it clearer. I confess I had sort of
found
the module but hadn't made sense of the documentation in relation to the
description
of embl/genbank feature descriptions. If it is of any use I could contribute
a couple
of lines and simple examples to the documentation to help (I may not be the
right person
for this though! )

kind regards

Sam

ps - I think there may be a ) missing from the ($feat->has_tag("note")) to
close? ;-)

Hilmar Lapp wrote:

> Samuel Aparicio wrote:
> >
> > Hi everyone
> > I am wondering if there is a method in Bioperl which allows access to
> > optional qualifiers with features in a genbank/embl entry. For example,
> > being able to parse out
> > the value of /note in the example below.
> >
> >  repeat_region   1586..1760
> >                      /note="L1M1 repeat: matches 5299..5484 of
> > consensus"
> >
>
> Bio::Seq has a method all_SeqFeatures(). For every element of the returned
> array (a Bio::SeqFeatureI compliant object) you can call
> has_tag("tag_name") and each_tag_value("tag_name") in order to query for
> existence and retrieve the values associated with a tag. So,
>
> foreach $feat ($seq->all_SeqFeatures()) {
>         if(($feat->primary_tag() eq "repeat_region") &&
>            ($feat->has_tag("note")) {
>                 foreach $val ($feat->each_tag_value("note")) {
>                         print "note: $val\n";
>                 }
>         }
> }
>
> Hope this helps. BTW the mentioned methods are documented in the perldoc
> pages of their modules (Bio::Seq and Bio::SeqFeature::Generic).
>
>         Hilmar
> --
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> -----------------------------------------------------------------

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