[BioC] Kegg Profile package problem

[Dan Tenenbaum]

On Thu, Dec 27, 2012 at 12:58 PM, gregory voisin <voisingreg at yahoo.fr> wrote:
>
> In that case, can you get the pathway map you need from this link:
> http://www.genome.jp/kegg/pathway/map/map00910.png ?
>
> In the automatic workflux  ( my case), it isn't very optimal
>
> I imagie that  download_KEGGfile function  concatenate
> (pathway_id="00910",specis='hsa') to build the request:
> 'http://www.genome.jp/kegg-bin/download?entry=hsa00910&format=kgml'
>
> Ideally the hsa could be replaced by "map".
>

I'm cc'ing the maintainer of the KEGGprofile package.

Dan


> Greg
>
>
>
> ________________________________
> De : Dan Tenenbaum <dtenenba at fhcrc.org>
> À : gregory voisin <voisingreg at yahoo.fr>
> Cc : "bioconductor at r-project.org" <bioconductor at r-project.org>
> Envoyé le : Jeudi 27 décembre 2012 14h39
>
> Objet : Re: [BioC] Kegg Profile package problem
>
> On Thu, Dec 27, 2012 at 4:30 AM, gregory voisin <voisingreg at yahoo.fr> wrote:
>> Hi Dan ,
>> Yes, the link associated to hsa00910 doesn't exist but the map00910
>> (http://www.genome.jp/kegg/pathway/map/map00910.html) exists
>>
>> The id 00910 is a result provided by the find_enriched_pathway function().
>>
>
> In that case, can you get the pathway map you need from this link:
>
> http://www.genome.jp/kegg/pathway/map/map00910.png
>
>
> ?
>
> Dan
>
>> Greg
>>
>>
>>
>> ________________________________
>> De : Dan Tenenbaum <dtenenba at fhcrc.org>
>> À : gregory voisin <voisingreg at yahoo.fr>
>> Cc : "bioconductor at r-project.org" <bioconductor at r-project.org>
>> Envoyé le : Jeudi 27 décembre 2012 2h35
>> Objet : Re: [BioC] Kegg Profile package problem
>>
>> 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
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>>
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>>
>>
>
>