[Bioperl-l] X.Y Fuzzy locations no longer supported in GenBank/EMBL/DDBJ

Brian Osborne bosborne11 at verizon.net
Wed Oct 18 11:13:51 EDT 2006


Chris,

No, I don't think they use the form X.Y. See below, from
t/LocationFactory.t, we do support most of the forms using ?. Supposedly
these tests accommodate all of the possible fuzzy locations encountered in
Swissprot, I wrote these a year or so ago.

Brian O.


        # UNCERTAIN locations and positions (Swissprot)
   "?2465..2774" => [$fuzzy_impl,
       2465, 2465, "UNCERTAIN", 2774, 2774, "EXACT", "EXACT", 1, 1],
   "22..?64" => [$fuzzy_impl,
       22, 22, "EXACT", 64, 64, "UNCERTAIN", "EXACT", 1, 1],
   "?22..?64" => [$fuzzy_impl,
       22, 22, "UNCERTAIN", 64, 64, "UNCERTAIN", "EXACT", 1, 1],
   "?..>393" => [$fuzzy_impl,
       undef, undef, "UNCERTAIN", 393, undef, "AFTER", "UNCERTAIN", 1, 1],
   "<1..?" => [$fuzzy_impl,
       undef, 1, "BEFORE", undef, undef, "UNCERTAIN", "UNCERTAIN", 1, 1],
   "?..536" => [$fuzzy_impl,
       undef, undef, "UNCERTAIN", 536, 536, "EXACT", "UNCERTAIN", 1, 1],
   "1..?" => [$fuzzy_impl,
       1, 1, "EXACT", undef, undef, "UNCERTAIN", "UNCERTAIN", 1, 1],
   "?..?" => [$fuzzy_impl,
       undef, undef, "UNCERTAIN", undef, undef, "UNCERTAIN", "UNCERTAIN", 1,
1],
   # Not working yet:
   #"12..?1" => [$fuzzy_impl,
   #    1, 1, "UNCERTAIN", 12, 12, "EXACT", "EXACT", 1, 1]





On 10/18/06 11:00 AM, "Chris Fields" <cjfields at uiuc.edu> wrote:

> Do they still use the X.Y notations?  Those are the most troublesome.  I
> guess we still don't support the ones containing '?'.
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
>> -----Original Message-----
>> From: Brian Osborne [mailto:bosborne11 at verizon.net]
>> Sent: Wednesday, October 18, 2006 9:43 AM
>> To: Chris Fields; bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] X.Y Fuzzy locations no longer supported in
>> GenBank/EMBL/DDBJ
>> 
>> Chris,
>> 
>> I'm fairly sure that Swissprot/Uniprot still supports fuzzy locations, all
>> of the more recent examples in t/LocationFactory.t come from there.
>> 
>> Brian O.
>> 
>> 
>> On 10/18/06 9:55 AM, "Chris Fields" <cjfields at uiuc.edu> wrote:
>> 
>>> EMBL/DDBJ formats are also dropping support for these 'fuzzy' locations.
>>> Not sure about UniProt/SwissProt.
> 
> 
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