[Bioperl-l] [EMBL reformatter problem with large acc_number]
Sebastien.Moretti at igs.cnrs-mrs.fr
Wed Dec 15 05:07:32 EST 2004
> > 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
> A small change to EMBL.pm should have you on your way without having to
> change any of your code.
Thanks, I works with the patch but it cuts my accession number.
So, it must be better to change
$temp_line = sprintf("%-11.10sstandard; $mol; $div; %d BP.", $seq->id(),
$temp_line = sprintf("%-10s standard; $mol; $div; %d BP.", $seq->id(), $len);
as reported at the end of the bur report.
I hope it will be fixed automatically in the 1.5 BioPerl release !
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