Re: [Gusdev-gusdev] LoadAnnotatedSeqs plugin underway

[Paul M. <pj...@sa...>]

>>> are there any other examples besides curation in which you have 
>>> placed structured data in qualifiers?     are there examples of 
>>> standard embl qualifiers in which you expect to find structured data 
>>> and parse it?
>>>
>>
>> After talking with Arnaud it seems we can take each 
>> qualifier/structured field and create a new feature, with each one of 
>> its qualifiers holding one piece of data. This would fit into your 
>> mapping scheme.
>>
> ok.  great.  i was wondering about that.

Arnaud had to point out the obvious to me :)

> so does that mean that we can expect that no qualifiers will contain 
> structured data that needs to be parsed?

We can make it so their is no structured data to be parsed (we'll leave 
it in but ignore it).

>>> about systematic_ids, i understand what you've said.   one thing 
>>> though.  how do they relate to gene names?
>>
>>
> ok, but, what i'm driving at is that the unflattener uses gene name 
> (/gene=) to decide what features go together in one gene model.   
> really, it wouldn't matter what the value of the /gene= is, as long as 
> it is identical for all features that belong to the gene.   is that 
> consistent with your use of /gene?

We don't use /gene until we submit to EMBL, when we convert 
/systematic_ids for /genes.
All EMBL files parsed into GUS have the previously mentioned name 
qualifiers.
Look at this extract of an EMBL file

FT CDS           1..3
FT               /systematic_id="name1"
.
.
FT CDS           4..8
FT               /temporary_systematic_id="name2"

Hence I need to tell the flattener to look for systematic_id first, 
then temporary_systematic_id.
It is important for us to use both.