[Biopython] zero-length feature
Peter
biopython at maubp.freeserve.co.uk
Tue Mar 23 12:43:57 UTC 2010
On Mon, Mar 22, 2010 at 3:38 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Mar 22, 2010 at 3:01 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>
>> All,
>>
>> Just to make sure I'm sanity-checked here, the GenBank/EMBL/DDBJ
>> location specs indicate a location of one nucleotide (inclusive) in length
>> is to be characterized as one number, not a range at all:
>>
>> http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#3.5.3
>>
>> 2..2
>>
>> should just be:
>>
>> 2
>>
>> Or, did I miss something in the discussion?
>>
>> chris
>
> On the face of it, I think you are right Chris. Good point.
>
> Peter
>
Hi again,
I've updated the trunk to handle single letter features like that.
This means the output of the example script I showed earlier
is now:
ID Test; ; ; DNA; ; UNC; 16 BP.
XX
AC Test;
XX
DE .
XX
OS .
OC .
XX
FH Key Location/Qualifiers
FT gap 2
FT /estimated_length=1
FT gap 4..5
FT /estimated_length=2
FT gap 7..9
FT /estimated_length=3
FT gap 11..15
FT /estimated_length=5
SQ Sequence 16 BP; 5 A; 0 C; 0 G; 0 T; 11 other;
ANANNANNNA NNNNNA 16
//
Note the single gap feature now has a location "2" not "2..2"
Thanks Chris,
Peter
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