[Bioperl-l] [EMBL reformatter problem with large acc_number]

simon andrews (BI) simon.andrews at bbsrc.ac.uk
Wed Dec 15 05:35:20 EST 2004

On 15 Dec 2004, at 10:07, Sebastien Moretti wrote:

>>> Hello,
>>> I use bioperl 1.4 on linux OS.
>>> I try to enhance some of my EMBL flat files with the standard EMBL
>>> reformatter
>>> of BioPerl:
>>> But some of my files have large accession number, like ensEMBL
>>> accession
>>> number, and my ID lines look like that:
>>> 	ID   ENSG00000156345standard; genomic DNA; UNK; 17425 BP.
>>> So, I would like to change this and to add blank spaces before
>>> 'standard;'.
>> This has been discussed on the list previously and there is a patch
>> waiting in bugzilla to sort out this behaviour
>> http://bugzilla.bioperl.org/show_bug.cgi?id=1618
>> A small change to EMBL.pm should have you on your way without having 
>> to
>> change any of your code.
>> Simon.
> Thanks, I works with the patch but it cuts my accession number.

See the modified patch at the bottom of the report which does exactly 
the same thing you did!

> I hope it will be fixed automatically in the 1.5 BioPerl release !

Hopefully it will be...


Simon Andrews PhD
Bioinformatics Dept.
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0) 1223 496463

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