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

[matthieu CONTE]

Ok...
But the method “get_BioDatabaseAdaptor” doesn't exist in the
Bio::DB::BioSQL::DBAdaptor module (documentation). I didn't find it on the 
bioperl-db web  page
    Any idea ?

Thanks



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: Wed, 28 Jan 2004 08:55:15 -0800
>
>I suspect you have an old version of bioperl-db, or a version mix-up. You 
>need to download and install the latest revision from CVS for bioperl-db.
>
>Note that if the root of the problem is with the pir parser then 
>load_seqdatabase.pl will not cure it, as it just uses any Bio::SeqIO 
>compliant parser to provide the input sequences. If the parser is broken 
>then there won't be input ... It just saves you the round-trip (and 
>possible errors associated with it) of going through swissprot format.
>
>	-hilmar
>
>On Wednesday, January 28, 2004, at 02:07  AM, matthieu CONTE wrote:
>
>>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
>>>>
>>>>_________________________________________________________________
>>>>MSN Messenger : discutez en direct avec vos amis ! 
>>>>http://www.msn.fr/msger/default.asp
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at portal.open-bio.org
>>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>--
>>>-------------------------------------------------------------
>>>Hilmar Lapp                            email: lapp at gnf.org
>>>GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>>>-------------------------------------------------------------
>>>
>>>
>>
>>_________________________________________________________________
>>MSN Messenger : discutez en direct avec vos amis ! 
>>http://www.msn.fr/msger/default.asp
>>
>>
>--
>-------------------------------------------------------------
>Hilmar Lapp                            email: lapp at gnf.org
>GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>-------------------------------------------------------------
>
>

_________________________________________________________________
MSN Search, le moteur de recherche qui pense comme vous ! 
http://search.msn.fr/worldwide.asp