Re: [GUSDEV] mapping file

[Steve F. <sfi...@pc...>]

the only documentation is:
  ga GUS::Supported::Plugin::InsertSequenceFeatures --help

plus, use the default mapping file, and the default special case handler 
(GUS::Supported::SpecialCaseQualifierHandler)

ask questions as they come up.

steve

Weichen Wu wrote:

> Where can I find more document about mapping file or 
> reportFeatureQualifiers? I will create a mapping file.
>
> Thanks,
> Weichen
>
> ----- Original Message ----- From: "Steve Fischer" 
> <sfi...@pc...>
> To: "Weichen Wu" <we...@se...>
> Cc: <gus...@li...>
> Sent: Saturday, October 08, 2005 7:29 AM
> Subject: Re: [GUSDEV] mapping file
>
>
>> yes, the mapping file is required.  you can use the genbank2gus.xml 
>> file if your embl file uses features and qualifiers that conform to 
>> the genbank/embl/ddbj feature table (see 
>> http://www.ncbi.nlm.nih.gov/collab/FT/).
>> but, you must understand that input often does not conform, or, 
>> places data into qualifiers in the wrong way.
>>
>> in this case, you will need to provide your own mapping file.
>>
>> here is a snip from the documentation from the plugin (i just 
>> improved the doc in latest plugin version):
>>
>> --------
>> Another way to generate a template mapping file is by using the 
>> command reportFeatureQualifiers.  This command analyzes a set of 
>> input files, and reports the feature/qualifier structure found in 
>> them.  It can output the report in simple text form, or in XML that 
>> is a template for the mapping file.
>> --------
>>
>> steve
>>
>> Weichen Wu wrote:
>>
>>> Hi,
>>>
>>> To use InsertSequenceFeatures plugin, is the mapping file is 
>>> required? There is a genebank2gus.xml. Is there a mapping file for 
>>> EMBL format available?
>>>
>>> Thanks,
>>> Weichen
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
>>> Power Architecture Resource Center: Free content, downloads, 
>>> discussions,
>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>> CenterStudy 0000600 0077645 0077645 00100322707 10322742046 012406  0 
>> ustar   wewu 0000000 0000000 From cets Tue May  3 15:23:11 2005
>> Date: 03 May 2005 15:23:11 -0400
>> From: Ask CETS <ce...@ho...>
>> Subject: DON'T DELETE THIS MESSAGE -- FOLDER INTERNAL DATA
>> Message-ID: <111...@ho...>
>> X-IMAP: 1101936235 0000000030
>> Status: RO
>>
>> Dear Email User,
>>
>> Hello!  My name is Paul Shaffer, and I'm a real person (not a computer
>> program).  I'm the "clerk" for the Eniac computer system here at SEAS.
>>
>> In order to keep track of your email, the computer needs to keep some
>> special directory information (things like which messages you've read).
>> This info is kept in an email message, which is kept in your 
>> mailbox.  In
>> fact, it is THIS VERY MESSAGE that keeps the directory info.
>>
>> Some other points you should know:
>>
>> + Don't delete this message - it will just come back if you do.
>>
>> + This message is created when you read mail using POP or IMAP, but
>>  you only see it when you read mail without POP or IMAP (e.g mutt or 
>> elm).
>>
>> + This message is like a bookmark.  POP or IMAP (the infrastructure that
>>  lets Netscape mail and Eudora work) creates it when you stop reading
>>  and looks for it when you start again.  It is stored here (rather than
>>  on your PC) so that you can use more than one machine and it will
>>  always be available.
>>
>> So, sit back, relax, and just IGNORE this message.  You need it.  You
>> can't get rid of it, so you might as well just get used to it.  If you
>> have any questions about what's going on, you can call 898-4707.
>>
>> Thank you for your understanding.
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev