[Bioperl-l] Bio ::seqIO ::tigr

[Hilmar Lapp]

A question aside: why do you want to convert to swissprot in order to 
load into biosql? (load_seqdatabase.pl can use any SeqIO reader.)

	-hilmar

On Tuesday, January 27, 2004, at 02:50  AM, matthieu CONTE wrote:

> I currently trying to use the Bio ::seqIO ::tigr module.
> My objective is to download the whole rice genome form Tigr ( adress 
> below)and to integrate it in my BioSQL DB.
> For this I am trying to convert the tigr format in swiss format with 
> the script below
>
>
> use Bio::SeqIO;
>
> my $in = Bio::SeqIO->new(-file 
> =>'</home/conte/pipeline_orthologues/data/orysa_tigr.txt', -format 
> =>'tigr');
>
> my $out = Bio::SeqIO->new(-file => 
> '>/home/conte/pipeline_orthologues/data/orysa_swiss.txt' , 
> -format=>'swiss');
>
> print $out $_ while <$in>;
>
> I obtain:
>
> ------------ EXCEPTION  -------------
> MSG: [19]Required <AUTHOR_LIST> missing
> STACK Bio::SeqIO::tigr::throw 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:1338
> STACK Bio::SeqIO::tigr::_process_header 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:700
> STACK Bio::SeqIO::tigr::_process_assembly 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:535
> STACK Bio::SeqIO::tigr::_process_tigr 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:453
> STACK Bio::SeqIO::tigr::_process 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:420
> STACK Bio::SeqIO::tigr::_initialize 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:90
> STACK Bio::SeqIO::new 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:358
> STACK Bio::SeqIO::new 
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:378
> STACK toplevel get_bioseq_tigr.pl:8
>
> Could you please tell me if there is a problem with the parser or with 
> the input data format of Tigr?
>
> Thanks in advance
>
>
>
>
> Matthieu CONTE
> m_conte at hotmail.com
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------