Please Show Me To Solve Import Problem Of Gitools

Question

[User 4391]

Hi,

I am using the Gitools for analysis sequences and I try to import data with Kegg but It has erro.

Description: Unable to connect to KEGG FTP: 450 /pub/kegg/genes/organisms/sce/: No such file or directory

trace: org.gitools.modules.importer.ModulesImporterException: Unable to connect to KEGG FTP: 450 /pub/kegg/genes/organisms/sce/: No such file or directory

Has anyone seen that erro? would you pleseas show me how to solve this problem? Thanks a lot.

Answer 1

[Sean Davis]

You might take a look here:

http://www.genome.jp/kegg/docs/plea.html

Just a guess, but it looks like Gitools might not have been updated to reflect the fact that KEGG has closed except to paid subscribers.

Answer 2

[Michi]

The importer has been fixed and a new version of Gitools has been released today!

Check it the blog post we released earlier today here: http://bg.upf.edu/blog/2012/02/gitools-database-importer-updates-kegg-and-ensembl/

[Istvan Albert]

sounds like is today is the original poster's lucky day

[Michi]

finally s/he can get back to work ;-)

Answer 3

[Christian Pérez-Llamas]

As Sean Davis told, KEGG ftp is for paid subscribers now.

Gitools needs to access the KEGG ftp to retrieve mappings between Ensembl gene id and KEGG gene id's.

I apologise for the inconvenience, but as soon as I know how to retrieve this information from other public source I will fix it.