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

[Hilmar Lapp]

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
>>>
>>> _________________________________________________________________
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>>>
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>>>
>>>
>> --
>> -------------------------------------------------------------
>> 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
-------------------------------------------------------------