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neeti somaiya | 18 Aug 13:41
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need help in parsing KEGG data

Hi,

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??

Thanks.

--

-- 
-Neeti
Even my blood says, B positive
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neeti somaiya | 18 Aug 14:13
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need help in parsing KEGG data

Hi,

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??

Thanks.

--

-- 
-Neeti
Even my blood says, B positive
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Mark Johnson | 18 Aug 15:26
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Re: need help in parsing KEGG data

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
...
...
...
(Continue reading)

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Mark Johnson | 18 Aug 15:29
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Re: need help in parsing KEGG data

On Mon, Aug 18, 2008 at 8:26 AM, Mark Johnson <johnsonm <at> gmail.com> wrote:

> 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:

Note that I downloaded
ftp://ftp.genome.jp/pub/kegg/genes/organisms/hsa/H.sapiens.ent and
provided the path to it as the argument to the script.
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neeti somaiya | 19 Aug 06:31
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Re: need help in parsing KEGG data

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
(Continue reading)

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