[BioC] Kegg Profile package problem

[Dan Tenenbaum]

On Wed, Dec 26, 2012 at 6:54 AM, gregory voisin <voisingreg at yahoo.fr> wrote:
>
>
>
> Hi,
> I use KeggProfile in my pipeline analysis and it's efficient, but I have problem with one pathway_ID.
>
> Exemple ( copy and paste):
>
> require(KEGGprofile)
> download_KEGGfile(pathway_id="04110",specis='hsa')
>
> #In this case , not problem
>
> download_KEGGfile(pathway_id="00910",specis='hsa')


I think perhaps there is no such pathway. Here's a list of all human pathways:
http://rest.kegg.jp/list/pathway/hsa

04110 is included but 00910 is not.

Dan


>
> #this pahway exits in KEGG, but the download is impossible
> #[1] "Downloading files: 1/1"
> #essai de l'URL 'http://www.genome.jp/kegg-bin/download?entry=hsa00910&format=kgml'
> #Content type 'text/plain' length unknown
> #URL ouverte
> #downloaded 1 bytes
>
> #essai de l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png'
> #Erreur dans download.file(paste("http://www.genome.jp/kegg/pathway/", specis,  :
> #  impossible d'ouvrir l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png'
> #De plus : Message d'avis :
> #In download.file(paste("http://www.genome.jp/kegg/pathway/", specis,  :
> #  ouverture impossible : le statut HTTP était '404 Not Found'
>
>
> My solution :  omit this pathway in my analysis: ponctual, fast  but not very elegant and not professional !!
>
> If someone has a suggestion , comments or solution, let's go ,
>
> Thanks
>
> Greg
> Montréal
>
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>
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