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

[Josh Lauricha]

Does the source_term_id refer to the source_tag()?

On Feb 26, 2004, at 9:08 AM, matthieu CONTE wrote:

> Ok I manage to use load_seqdatabase !
> But....there is another problem.......
> There is null field and I think Biosql don’t accept this.
> Table Seqfeature id : field 'source_term_id'
>
> Do you think  it will be better to make modifications on the  
> tigrxml.dtd or on the load_seqdatabase script?
>
>
> [conte at bearn biosql]$ perl load_seqdatabase.pl --dbuser biosql  
> --dbpass biosql --namespace orysa_tigr --format tigr  
> /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml
> Loading /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,  
> values were ("","1") FKs (26216,37,<NULL>)
> Column 'source_term_id' cannot be null
> ---------------------------------------------------
> Could not store 8355.t01530:
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::SeqFeature::Generic) failed to insert or to  
> be found by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children  
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ 
> SeqAdaptor.pm:246
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:215
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) load_seqdatabase.pl:517
> STACK toplevel load_seqdatabase.pl:500
>
>
>
>
>
>
>
>
> -----------------------------------------------------------
> Matthieu CONTE
> M. Sc. in Bioinformatics from SIB
>
> CIRAD-Biotrop TA40/03
> Avenue Agropolis
> 34398 Montpellier Cedex 5
> FRANCE
>
> m_conte at hotmail.com
> tel: (33)04 67 61 60 21
> fax :(33) 4 67 61 56 05
>
> -----------------------------------------------------------
>
>
>
>
>
>> From: Josh Lauricha <laurichj at cs.ucr.edu>
>> To: "matthieu CONTE" <m_conte at hotmail.com>
>> Subject: Re: [Bioperl-l] Re: Bio ::seqIO ::tigr Date: Wed, 25 Feb  
>> 2004 08:50:39 -0800
>>
>> Thanks for pointing out the typos (the other one is my e-mail address  
>> ;).
>>
>> However, based on the size of the file your using (the error is at  
>> line 2892), I am willing to bet they are the .coordset files. These  
>> are not the Tigr XML format. Actually, they are not even valid XML...  
>> If this is the case (check by the extention or, if still in doubt,  
>> open them up. If there is a <TIGR> tag on the first line then its an  
>> error in my parser), Jason wrote a parser for this that I can send to  
>> you.
>>
>> On Feb 25, 2004, at 8:02 AM, matthieu CONTE wrote:
>>
>>> Hi,
>>> I tried your version of tigr.pm Mr Lauricha. There is a typing  
>>> mistake line 820.
>>>
>>> unfortunately it still have another  problem:
>>> "MSG: [2892]Required <ASSEMBLY_SEQUENCE> missing"
>>>
>>> -----------------------------------------------------------
>>> Matthieu CONTE
>>> M. Sc. in Bioinformatics from SIB
>>>
>>> CIRAD-Biotrop TA40/03
>>> Avenue Agropolis
>>> 34398 Montpellier Cedex 5
>>> FRANCE
>>>
>>> m_conte at hotmail.com
>>> tel: (33)04 67 61 60 21
>>> fax :(33) 4 67 61 56 05
>>>
>>> -----------------------------------------------------------
>>>
>>> _________________________________________________________________
>>> MSN Messenger : discutez en direct avec vos amis !  
>>> http://www.msn.fr/msger/default.asp
>>>
>>>
>> Josh Lauricha
>> laurichj at bioinfo.ucr.edu
>> OpenPGP: 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8
>> << PGP.sig >>
>
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>
Josh Lauricha
laurichj at bioinfo.ucr.edu
OpenPGP: 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8

Josh Lauricha
laurichj at bioinfo.ucr.edu
OpenPGP: 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8
Josh Lauricha
laurichj at bioinfo.ucr.edu
OpenPGP: 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8
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