Re: KEGG

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Re: KEGG

Stephen Ficklin-2
Hi Zhensheng,

I'm CC'ing your email to the mailing list in case others have a similar problem.

I'm looking at the messages you pasted below.  Do you have sequences named 'AE_Aech_01080' and 'AE_Aech_10533'?  If so, one problem is that your regular expression is not correct.  Try this instead: 

^(.*)$

That should pick up the entire feature name in the KEGG heir file and try to use it to match against features in the database. 

However, I think there may be a bug, because if you do have matching feature names in your KEGG file and in the database you shouldn't have to enter a regular expression at all.  Let me know.

Thanks,
Stephen



On 2/7/2012 9:54 PM, 陈镇生 wrote:
Hi  Stephen,

I face the challenge about the KEGG :
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_01080
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10533
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10464
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_08894

Recent log entries:

MessageDivision by zero in /var/www/html/acromyrmex/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 424.


Thanks,
Zhensheng



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Re: KEGG

Chun-Huai Cheng
Hi Zhensheng,

Are you trying to load the KEGG analysis results? The KEGG module reads in the 'heir.tar.gz' file generated by the KEGG KAAS server (http://www.genome.ad.jp/tools/kaas/). Can you untar and check if your file is intact? There should be a couple of .keg files after you untar it.

Thanks,

Chun-Huai

2012/2/7 Stephen Ficklin <[hidden email]>
Hi Zhensheng,

I'm CC'ing your email to the mailing list in case others have a similar problem.

I'm looking at the messages you pasted below.  Do you have sequences named 'AE_Aech_01080' and 'AE_Aech_10533'?  If so, one problem is that your regular expression is not correct.  Try this instead: 

^(.*)$

That should pick up the entire feature name in the KEGG heir file and try to use it to match against features in the database. 

However, I think there may be a bug, because if you do have matching feature names in your KEGG file and in the database you shouldn't have to enter a regular expression at all.  Let me know.

Thanks,
Stephen



On 2/7/2012 9:54 PM, 陈镇生 wrote:
Hi  Stephen,

I face the challenge about the KEGG :
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_01080
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10533
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10464
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_08894

Recent log entries:

MessageDivision by zero in /var/www/html/acromyrmex/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 424.


Thanks,
Zhensheng



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Re: 答复: KEGG

Chun-Huai Cheng
Hello Zhensheng,

Would you mind sharing how you solved the problem as this might benefit other users?


Thanks,

Chun-Huai

2012/2/7 陈镇生 <[hidden email]>
Hi Chun-Huai,

Thank you for your reply ,and the problem have  been solved .

Thanks
Zhensheng

发件人: Chun-Huai Cheng [[hidden email]]
发送时间: 2012年2月8日 14:52
到: [hidden email]
主题: Re: [Gmod-tripal] KEGG

Hi Zhensheng,

Are you trying to load the KEGG analysis results? The KEGG module reads in the 'heir.tar.gz' file generated by the KEGG KAAS server (http://www.genome.ad.jp/tools/kaas/). Can you untar and check if your file is intact? There should be a couple of .keg files after you untar it.

Thanks,

Chun-Huai

2012/2/7 Stephen Ficklin <[hidden email]>
Hi Zhensheng,

I'm CC'ing your email to the mailing list in case others have a similar problem.

I'm looking at the messages you pasted below.  Do you have sequences named 'AE_Aech_01080' and 'AE_Aech_10533'?  If so, one problem is that your regular expression is not correct.  Try this instead: 

^(.*)$

That should pick up the entire feature name in the KEGG heir file and try to use it to match against features in the database. 

However, I think there may be a bug, because if you do have matching feature names in your KEGG file and in the database you shouldn't have to enter a regular expression at all.  Let me know.

Thanks,
Stephen



On 2/7/2012 9:54 PM, 陈镇生 wrote:
Hi  Stephen,

I face the challenge about the KEGG :
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_01080
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10533
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10464
Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_08894

Recent log entries:

MessageDivision by zero in /var/www/html/acromyrmex/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 424.


Thanks,
Zhensheng



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is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
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Re: 答复: 答复: KEGG

Chun-Huai Cheng

Thank you for sharing Zhensheng. :)

Chun-Huai
On Feb 7, 2012 11:52 PM, "陈镇生" <[hidden email]> wrote:
>
> Hi Chun-Huai,
>
> It is the matching problem,and I fill  the  regular expression in the Query Name RE:
>
> Thanks,
> Zhensheng
> ________________________________
> 发件人: Chun-Huai Cheng [[hidden email]]
> 发送时间: 2012年2月8日 15:45
> 到: [hidden email]
> 主题: Re: [Gmod-tripal] 答复: KEGG
>
> Hello Zhensheng,
>
> Would you mind sharing how you solved the problem as this might benefit other users?
>
>
> Thanks,
>
> Chun-Huai
>
> 2012/2/7 陈镇生 <[hidden email]>
>>
>> Hi Chun-Huai,
>>
>> Thank you for your reply ,and the problem have  been solved .
>>
>> Thanks
>> Zhensheng
>> ________________________________
>> 发件人: Chun-Huai Cheng [[hidden email]]
>> 发送时间: 2012年2月8日 14:52
>> 到: [hidden email]
>> 主题: Re: [Gmod-tripal] KEGG
>>
>> Hi Zhensheng,
>>
>> Are you trying to load the KEGG analysis results? The KEGG module reads in the 'heir.tar.gz' file generated by the KEGG KAAS server (http://www.genome.ad.jp/tools/kaas/). Can you untar and check if your file is intact? There should be a couple of .keg files after you untar it.
>>
>> Thanks,
>>
>> Chun-Huai
>>
>> 2012/2/7 Stephen Ficklin <[hidden email]>
>>>
>>> Hi Zhensheng,
>>>
>>> I'm CC'ing your email to the mailing list in case others have a similar problem.
>>>
>>> I'm looking at the messages you pasted below.  Do you have sequences named 'AE_Aech_01080' and 'AE_Aech_10533'?  If so, one problem is that your regular expression is not correct.  Try this instead: 
>>>
>>> ^(.*)$
>>>
>>> That should pick up the entire feature name in the KEGG heir file and try to use it to match against features in the database. 
>>>
>>> However, I think there may be a bug, because if you do have matching feature names in your KEGG file and in the database you shouldn't have to enter a regular expression at all.  Let me know.
>>>
>>> Thanks,
>>> Stephen
>>>
>>>
>>>
>>> On 2/7/2012 9:54 PM, 陈镇生 wrote:
>>>>
>>>> Hi  Stephen,
>>>>
>>>> I face the challenge about the KEGG :
>>>> Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_01080
>>>> Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10533
>>>> Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_10464
>>>> Failed: '' cannot find a matching feature in the databasef.  RE: AE_Aech; LINE: AE_Aech_08894
>>>>
>>>> Recent log entries:
>>>>
>>>> MessageDivision by zero in /var/www/html/acromyrmex/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 424.
>>>>
>>>>
>>>> Thanks,
>>>> Zhensheng
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Keep Your Developer Skills Current with LearnDevNow!
>>> The most comprehensive online learning library for Microsoft developers
>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>> http://p.sf.net/sfu/learndevnow-d2d
>>> _______________________________________________
>>> Gmod-tripal mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>
>


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