lomSpace has asked for the wisdom of the Perl Monks concerning the following question:

Hello,
I am using Bio::Graphics and Bio::SeqIO modules to process a genbank file.
How do I process some and not all of the values from an array reference?
# sorts each feature by its primary tag into a hash 
# of array references named %sorted_features
my %sorted_features;
for my $f (@features) {
  #get cds, primer_bind, and genes features only
  my $tag = $f->primary_tag;
  # create a hash of $f keys and $tag values
  push @{$sorted_features{$tag}},$f;
}

[download]
There are several features: CDS,exons, genes, mRNAs, misc_RNAs
primer_binds,repeat_regions, and sources. I am only interested in processing
CDS, genes, and primer_binds, and sources.

Presently, all of the features are processed and output to the graphics file.

Any examples would be greatly appreciated.
Lom Space

Replies are listed 'Best First'.
Re: processing data from an array reference
by graff (Chancellor) on Jul 23, 2009 at 05:28 UTC
    Do you mean that when you do this step: 
       my $tag = $f->primary_tag;

    [download]
    the value of $tag is one of: CDS, exons, genes, mRNAs, misc_RNAs, primer_binds, repeat_regions, or sources?

    If that's what is happening, all you need to do is place a condition on the following "push" -- only do the push if the value of $tag is one that you want: 

        push @{$sorted_features{$tag}}, $f if ($tag =~ /CDS|genes|primer_b
+inds|sources/);

    [download]
    Or, if you prefer, you can create a hash whose keys are the desired set of feature names, and then the condition can check for the hash key, instead of doing a regex match: 
    my %sorted_features;
my %want = map { $_ => 1 } qw/CDS genes primer_binds sources/;
for my $f ( @features ) {
    my $tag = $f->primary_tag;
    push @{$sorted_features{$tag}}, $f if( $want{$tag} );
}

    [download]
[reply]
[d/l]
[select]
Re: processing data from an array reference
by Anonymous Monk on Jul 23, 2009 at 05:05 UTC
[reply]

Back to Seekers of Perl Wisdom