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

[Hilmar Lapp]

That's why I said you seem to have a version mix-up in addition.  
get_BioDatabaseAdaptor is part of the 0.1 API, which was retired more  
than a year ago.

	-hilmar

On Monday, February 2, 2004, at 04:11  AM, matthieu CONTE wrote:

>
> 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
>>>>>
>>>>> _________________________________________________________________
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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 !  
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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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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------