tripal demo kegg analysis not working

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tripal demo kegg analysis not working

Moore, Gary

Still working my way through the v0.31b demo and am experiencing an issue with loading Flybase-tripal-demo.kegg.heir.tar.gz.    I’m thinking the basic problem is that no feature matches are being found.  I base this on the code in the tripal_analysis_kegg_check_line_handle_feature function which uses a regex to extract features from lines in the hier files:

 

if(preg_match("/^(.*?);\s*(\<a.+)/",$value,$matches)){

      $has_feature = 1;

      $fname = $matches[1];

      $keggterm = $matches[2];

 

In this case the preg_match is always false.   Further, eyeballing the hier files, I don’t see anything which might match this regex.  I’m out of ideas at the moment and would appreciate any help.

Thanks

Gary

 

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





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Re: tripal demo kegg analysis not working

Stephen Ficklin-2
Hi Gary,

It looks as though that KEGG hier file on the tutorial has no matches in it.  Which is why it is not pulling out any matches. 

We never did get to loading the KEGG data into Tripal during the courses where this tutorial was used.  So, it may be that for the small selection of genes used for the tutorial that there are no KEGG matches, and it was never noticed.   I'll try to rebuild the file and see if I can correct the files on the tutorial. 

But, the KEGG module does work as described in the tutorial as we use it  on our production sites.  So, feel free to move along with the tutorial and when it comes time to load your own data with KEGG analyses it should work as described.

Stephen

On 5/11/2012 2:30 PM, Moore, Gary wrote:

Still working my way through the v0.31b demo and am experiencing an issue with loading Flybase-tripal-demo.kegg.heir.tar.gz.    I’m thinking the basic problem is that no feature matches are being found.  I base this on the code in the tripal_analysis_kegg_check_line_handle_feature function which uses a regex to extract features from lines in the hier files:

 

if(preg_match("/^(.*?);\s*(\<a.+)/",$value,$matches)){

      $has_feature = 1;

      $fname = $matches[1];

      $keggterm = $matches[2];

 

In this case the preg_match is always false.   Further, eyeballing the hier files, I don’t see anything which might match this regex.  I’m out of ideas at the moment and would appreciate any help.

Thanks

Gary

 

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





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Re: tripal demo kegg analysis not working

Moore, Gary

Thanks, Stephan.   Having moved on in the tutorial, I have one more issue which I will send in a subsequent post.  Thanks again for your help.

Gary

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Monday, May 14, 2012 12:37 PM
To: Moore, Gary
Cc: [hidden email]
Subject: Re: [Gmod-tripal] tripal demo kegg analysis not working

 

Hi Gary,

It looks as though that KEGG hier file on the tutorial has no matches in it.  Which is why it is not pulling out any matches. 

We never did get to loading the KEGG data into Tripal during the courses where this tutorial was used.  So, it may be that for the small selection of genes used for the tutorial that there are no KEGG matches, and it was never noticed.   I'll try to rebuild the file and see if I can correct the files on the tutorial. 

But, the KEGG module does work as described in the tutorial as we use it  on our production sites.  So, feel free to move along with the tutorial and when it comes time to load your own data with KEGG analyses it should work as described.

Stephen

 





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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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