[Bioperl-l] Error in loading into biosql database

[Hilmar Lapp]

If you dropped it and re-created it that should have taken care of 
records erroneously without NCBI taxon ID.

To verify you can query before an upload:

	mysql> SELECT binomial, variant, ncbi_taxon_id FROM taxon WHERE 
ncbi_taxon_id IS NULL;

To confirm for Homo sapiens:

	mysql> SELECT * FROM taxon WHERE binomial = 'Homo sapiens' AND
	(ncbi_taxon_id IS NULL OR ncbi_taxon_id != 9606)

Neither of the 2 queries should return any rows.

If they don't and you still get this error then look in your input file 
for the first occurrence of Homo sapiens as species for the sequence. 
Does it come with NCBI taxon ID? If no, here is your problem. If yes, 
look for the second sequence of Homo sapiens. Does it have accession# 
P42655? If yes (*), truncate the taxon table and create a new input 
file with only the first Homo sapiens sequence entry (which supposedly 
has a taxon ID). Try to load the single-entry file. After that, check 
your taxon table. There should be Homo sapiens. If it lacks the NCBI 
taxon ID (*), the problem is with the parser not parsing the taxon ID 
out of the input.

(*) if you have to answer 'no' here, there's possibly something weird 
going that would need to be fully debugged. You can try to run 
load_seqdatabase.pl with --debug and send me the output.

	-hilmar

On Wednesday, March 19, 2003, at 02:23  PM, Siddhartha Basu wrote:

> Hi,
>
>
> Hilmar Lapp wrote:
>> Log on to mysql and type
>>     mysql> show variables;
>> Then look for those that match /innodb/. Do these look alright? 
>> Specifically, does the variable have_innodb show with a value of YES?
> Yes they look alright and the variable 'have_innodb' is set to YES.
>
>> Transactions are enabled if innodb is enabled. The tables are type 
>> INNODB.
> In my mysql database innodb is enabled as i see the log files and dat 
> files in /var/lib/mysql as pointed out by mysql manual.
>> When you say you remove entries prior to inserting new ones, what do 
>> you mean? Do you remove bioentries, supply --remove to 
>> load_seqdatabase.pl, purge the entire biosql database, or truncate 
>> the taxon table? *Only* the two latter will remove rows from the 
>> taxon table.
> I droped the biosql database not purged it. I haven't used the other 
> two options. Do i have to purge the database instead of dropping it.
>
> siddhartha
>
>
>>     -hilmar
>
>
-- 
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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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