Hi Feifei,

You could write a perl script to sort the tags after saving from
Artemis.  It wouldn't be too hard I imagine, though I wouldn't suggest
using BioPerl to do it, as I don't think you can guarantee the order
of tags when the GFF3 methods write them out either.

Scott


On Tue, Sep 20, 2011 at 2:42 AM, Feifei Xu <feifei...@ebc.uu.se> wrote:
> Yes. I am using the gff3 file as the base for manual annotation. I am keeping 
> it versioned to keep track of what has been changed. So if there is no way to 
> retain the order of attributes, it's just killing the the version system.
>
> So far I managed to retain the order by changing "accession_id" to something 
> else. But it would be good to know how Artemis saves gff3 files. I need to 
> know if the order will always be retained, or it's just purely random?
>
> BTW, is there any way to auto save the gff3 file in artemis?
>
> Thanks!
> Feifei
>
> On 19 sep 2011, at 18.01, Scott Cain wrote:
>
>> Hi Feifei,
>>
>> Is there a reason you want to retain order?  The order of attributes
>> should not matter.
>>
>> Scott
>>
>>
>> On Mon, Sep 19, 2011 at 11:11 AM, Feifei Xu <feifei...@ebc.uu.se> wrote:
>>> Hi!
>>>
>>> Is there any way to conserve the order of the attributes (column 9) in gff3 
>>> file?
>>>
>>> The problem I have now is between the two tags "label" and "accession_id". 
>>> If I load a version (v1) of gff3 file with "label" before "accession_id", 
>>> then it will be saved into a new version (v2) of gff3 file with 
>>> "accession_id" before "label".  When I thought that I can live with the 
>>> order in v2, and tried to save v2 into yet another version (v3), then the 
>>> order changed back to  "label" before "accession_id".
>>>
>>> It would be great if there is any way to fix the order. I will also try to 
>>> change the tags, see if that will do.
>>>
>>> Thanks!
>>>
>>> Feifei
>>> _______________________________________________
>>> Artemis-users mailing list
>>> Artemis-users@sanger.ac.uk
>>> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot 
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
> _______________________________________________
> Artemis-users mailing list
> Artemis-users@sanger.ac.uk
> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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