bio/scripts/get_uniprot error

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bio/scripts/get_uniprot error

wang su
Hi,
I want to use bio/scripts/get_uniprot to download the special taxonID with uniprot data, before do this, I had installed all the perl Modules listed in http://intermine.org/wiki/InstallingPerlModules#ListofPerlModulestoInstall, but there still have errors said 'can't locate InterMine/DataDownloader, then I use bio/scripts/DataDownloader/bin/download_data -e **mine, still have erros said Can't locate Path/Class.pm, then I use cpan Path::Class to install this module. I don't know how to solve this problem~
Can you help me?
Many thanks!

Su
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Fwd: bio/scripts/get_uniprot error

wang su
I think if you have the 9606_uniprot_sprot.xml 9606_uniprot_trembl.xml and 10090_uniprot_sprot.xml, 10090_uniprot_tremble.xml, could you please give me a link to download it directly.

Thanks

Begin forwarded message:

From: wang su <[hidden email]>
Date: 2012年1月16日 下午02时45分08秒格林尼治标准时间+0800
Subject: bio/scripts/get_uniprot error

Hi,
I want to use bio/scripts/get_uniprot to download the special taxonID with uniprot data, before do this, I had installed all the perl Modules listed in http://intermine.org/wiki/InstallingPerlModules#ListofPerlModulestoInstall, but there still have errors said 'can't locate InterMine/DataDownloader, then I use bio/scripts/DataDownloader/bin/download_data -e **mine, still have erros said Can't locate Path/Class.pm, then I use cpan Path::Class to install this module. I don't know how to solve this problem~
Can you help me?
Many thanks!

Su


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Re: Fwd: bio/scripts/get_uniprot error

Julie Sullivan
The download scripts have stopped working for me too, I'm not sure what's going
on but these are the URLs the scripts use:

// 9606_uniprot_sprot
http://www.uniprot.org/uniprot/?format=xml&query=taxonomy%3A9606+AND+reviewed%3Ayes&compress=yes 


change the "reviewed" parameter to get trembl proteins

// 9606_uniprot_trembl
http://www.uniprot.org/uniprot/?format=xml&query=taxonomy%3A9606+AND+reviewed%3Ano&compress=yes 


change the taxon ID to get mouse instead of human

// 10090_uniprot_sprot
http://www.uniprot.org/uniprot/?format=xml&query=taxonomy%3A10090+AND+reviewed%3Ayes&compress=yes 


// 10090_uniprot_trembl
http://www.uniprot.org/uniprot/?format=xml&query=taxonomy%3A10090+AND+reviewed%3Ano&compress=yes 


Here are the docs on the UniProt web services if you want more information:

http://www.uniprot.org/faq/28


On 16/01/12 08:15, wang su wrote:

> I think if you have the 9606_uniprot_sprot.xml 9606_uniprot_trembl.xml and 10090_uniprot_sprot.xml, 10090_uniprot_tremble.xml, could you please give me a link to download it directly.
>
> Thanks
>
> Begin forwarded message:
>
>> From: wang su<[hidden email]>
>> Date: 2012年1月16日 下午02时45分08秒格林尼治标准时间+0800
>> To: [hidden email]
>> Subject: bio/scripts/get_uniprot error
>>
>> Hi,
>> I want to use bio/scripts/get_uniprot to download the special taxonID with uniprot data, before do this, I had installed all the perl Modules listed in http://intermine.org/wiki/InstallingPerlModules#ListofPerlModulestoInstall, but there still have errors said 'can't locate InterMine/DataDownloader, then I use bio/scripts/DataDownloader/bin/download_data -e **mine, still have erros said Can't locate Path/Class.pm, then I use cpan Path::Class to install this module. I don't know how to solve this problem~
>> Can you help me?
>> Many thanks!
>>
>> Su
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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Re: Fwd: bio/scripts/get_uniprot error

Vallejos, Andrew
In reply to this post by wang su

You could also use the get_and_split_uniprot.pl script.  It pre-dates the get_uniprot, and may be less efficient, but it should work in downloading the XML documents you require.

 

-Andrew

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of wang su
Sent: Monday, January 16, 2012 2:15 AM
To: [hidden email]
Subject: [InterMine Dev] Fwd: bio/scripts/get_uniprot error

 

I think if you have the 9606_uniprot_sprot.xml 9606_uniprot_trembl.xml and 10090_uniprot_sprot.xml, 10090_uniprot_tremble.xml, could you please give me a link to download it directly.

 

Thanks

 

Begin forwarded message:



From: wang su <[hidden email]>

Date: 2012116 下午024508秒格林尼治标准时间+0800

Subject: bio/scripts/get_uniprot error

 

Hi,
I want to use bio/scripts/get_uniprot to download the special taxonID with uniprot data, before do this, I had installed all the perl Modules listed in http://intermine.org/wiki/InstallingPerlModules#ListofPerlModulestoInstall, but there still have errors said 'can't locate InterMine/DataDownloader, then I use bio/scripts/DataDownloader/bin/download_data -e **mine, still have erros said Can't locate Path/Class.pm, then I use cpan Path::Class to install this module. I don't know how to solve this problem~
Can you help me?
Many thanks!

Su

 


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