[Bioperl-l] need help in parsing KEGG data

neeti somaiya neetisomaiya at gmail.com
Tue Aug 19 00:31:28 EDT 2008


Thanks a lot for the reply. It was a problem of the bioperl version.

~Neeti.

On Mon, Aug 18, 2008 at 6:56 PM, Mark Johnson <johnsonm at gmail.com> wrote:

> On Mon, Aug 18, 2008 at 6:45 AM, neeti somaiya <neetisomaiya at gmail.com>
> wrote:
>
> > I am fetching data from the ent gene file of KEGG which is available here
> :
> > ftp://ftp.genome.jp/pub/kegg/genes/organisms/hsa/H.sapiens.ent
> >
> > I am using Bio::SeqIO with file format of type KEGG. I am trying to fetch
> > gene names and pathways in which they participate. I am getting the gene
> > names fine. But this method
> >
> > "for my $pathway ( $seq->annotation->get_Annotations('pathway') ){
> > }"
> >
> > does'nt seem to be working. I am not able to get the data of the pathways
> in
> > which the gene is involved.
> >
> > Can someone please suggest how I can get the pathway data of genes from
> the
> > KEGG ent file??
>
> What exactly do you mean by "doesn't seem to be working" and what
> version of BioPerl are you using?  The code below seems to function as
> expected with BioPerl 1.5.2, producing output like this:
>
> hsa04612  Antigen processing and presentation
> hsa01430  Cell Communication
> hsa04020  Calcium signaling pathway
> hsa04080  Neuroactive ligand-receptor interaction
> hsa04540  Gap junction
> ...
> ...
> ...
>
> #!/wherever/bin/perl
>
> use strict;
> use warnings;
>
> use Bio::SeqIO;
>
>
> my $seqio = Bio::SeqIO->new(-format => 'kegg', -file => $ARGV[0]);
>
> while (my $seq = $seqio->next_seq()) {
>
>    foreach my $pathway ($seq->annotation->get_Annotations('pathway')) {
>
>        ## $pathway should be a Bio::Annotation::Comment
>        print $pathway->text(), "\n";
>
>    }
>
> }
>



-- 
-Neeti
Even my blood says, B positive


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