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

[matthieu CONTE]

Ok , I try directly with "load_seqdatabase.pl"  but there is another 
problem.....

[conte at bearn scripts]$  perl load_seqdatabase.pl -dbuser biosql -dbpass 
biosql -format tigr tigr 
/home/conte/pipeline_orthologues/data/orysa_tigr.txt

Can't locate object method "get_BioDatabaseAdaptor" via package 
"Bio::DB::BioSQL::DBAdaptor" at load_seqdatabase.pl line 84.

Indeed this method does not exist in Bio::DB::BioSQL::DBAdaptor....




Matthieu CONTE
M. Sc. in Bioinformatics from SIB

00 33 06.68.90.28.70
m_conte at hotmail.com





>From: Hilmar Lapp <hlapp at gmx.net>
>To: "matthieu CONTE" <m_conte at hotmail.com>
>CC: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] Bio ::seqIO ::tigr Date: Tue, 27 Jan 2004 09:31:39 
>-0800
>
>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
>-------------------------------------------------------------
>
>

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