[Bioperl-l] genbank parsing of multiple 'function' tags within primary tag

[galeb abu-ali]

many thanks again, Chris! I was reading Programming Perl, but this sums it
up better.

On Thu, Sep 8, 2011 at 2:27 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

> On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:
>
> > thanks, Chris! works perfect.
> > To make sure I understand what's going on, forcing list context on $locus
> allows me to get one value at a time,...
>
> You have to be careful in this circumstance; doing this:
>
>   my $foo = @bar;
>
> is scalar context on a list, which returns the number of elements in @bar.
>  The following
>
>   my ($foo) = @bar;
>
> forces list context and assigns the first value in @bar to $foo but tosses
> the rest.  If you are sure there is only one value in @bar anyway, the above
> is fine (and is a common perl idiom).
>
> > which is then concatenated with \t to concatenated functions.
>
> I'm just using a simple join() to print off the results.  Note the second
> element in the join list is an embedded join() with comma-sep values for
> functions.
>
> chris
>
> > thanks again!
> >
> > galeb
> >
> > On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
> > There is no need to do that if one is using the Bio::SeqFeatureI
> interface.  Note that get_tag_values always returns a list, so to snag a
> single value for a tag in a scalar, force list context on the LHS by
> enclosing the variable in ().
> >
> > chris
> >
> > -----------------------------
> > #!/usr/bin/env perl
> >
> > use Modern::Perl;
> > use Bio::SeqIO;
> >
> > my $in = Bio::SeqIO->new(-format => 'genbank',
> >                         -file => shift);
> >
> > while (my $seq = $in->next_seq) {
> >   for my $feat ($seq->get_SeqFeatures) {
> >       next unless $feat->primary_tag eq 'CDS';
> >       my ($locus) = $feat->has_tag('locus_tag') ?
> >                     $feat->get_tag_values('locus_tag') : '';
> >       my @funcs = $feat->has_tag('function') ?
> >           $feat->get_tag_values('function') : ();
> >       say join("\t", $locus, join(',', at funcs));
> >   }
> > }
> >
> >
> >
>
>