[Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

Dan Bolser dan.bolser at gmail.com
Wed Jul 14 06:27:02 EDT 2010


Hi Jason,

Thanks for the suggestion (see below).

On 13 July 2010 23:48, Jason Stajich <jason at bioperl.org> wrote:
> Dan -
> I'm not convinced that contig:example is proper type/source for the
> landmarks & scaffold - i use 'scaffold:chromosome' in my data:
>
> What happens if you change the GFF3 file line from
> ctgA example contig 1 50000 . . . Name=ctgA
> to
> ctgA chromosome scaffold 1 50000 . . . Name=ctgA
>
>
> I think this can be tweaked in the config but there may be different
> defaults for the in memory and DBI::mysql implementation.

I found that this doesn't make any difference, however, I have found
more information about what causes the bug.

>From my previous email you see that I use bp_seqfeature_load.pl with
the "--namespace volvox" option (I should have guessed it was
something to do with this). Looking closely at the resulting tables I
see that the following tables are empty

volvox_attribute
volvox_parent2child
volvox_feature
volvox_interval_stats
volvox_name
volvox_parent2child


they are not empty when created without the "--namespace x" prefix,
which is why DBI::mysql 'normally' works.

All the other tables:

volvox_attributelist
volvox_locationlist
volvox_meta
volvox_sequence
volvox_typelist


appear to be created correctly, with or without the "--namespace x" prefix.


Cheers,
Dan.

> -jason
> Dan Bolser wrote, On 7/13/10 12:49 AM:
>
> Cheers Chris,
>
> Is there a known good version of
> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to?
> I believe that this is one of the more common databases, so I'm
> surprised to find it broken.
>
> What would be the git command to roll back to a stable BioPerl / GBrowse?
>
>
> Sorry for the basic questions,
> Dan.
>
> On 12 July 2010 17:56, Chris Fields <cjfields at illinois.edu> wrote:
>
>
> Dan.
>
> Is this maybe something for the GBrowse list? (cc'ing there JIC)
>
> chris
>
> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:
>
>
>
> Seems I still can't log bugs here:
> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474
>
> Error:
>        Artifact: Only Artifact Admins Can Modify Private ArtifactTypes
>
>
> Here I my bug report:
>
> I'm following the tutorial here:
>
> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html
>
>
> I successfully set up and browsed the first database (going no further
> than #data_file). I decided to try switching from an in memory
> (file-based) database to a DBI::mysql database. After taking the
> appropriate steps (see below), I get the following error when viewing
> the database in GB:
>
>        The landmark named ctgA is not recognized. See the help pages
> for suggestions.
>
>
> I'm not sure why the landmark is found using a memory (file-based)
> database, but not found when using the same GFF loaded into mysql.
>
> This is the latest bioperl-live (although I'm still struggling with git).
>
> Any hints on what might be going wrong? I've a feeling I should
> perhaps roll back a few versions, as I noticed some SQL errors coming
> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm".
>
>
> Cheers,
> Dan.
>
>
>
> 1) I loaded the GFF:
>
> bp_seqfeature_load.pl -v -v -f -c -z \
>  --dsn dbi:mysql:mydb:myhost \
>  --namespace volvox \
> --summary \
>  -u me -p secret \
> databases/volvox/volvox_remarks.gff3
>
>
> 2) I changed the volvox.conf file:
>
> #db_args       = -adaptor memory
> #               -dir '$HTDOCS/databases/volvox'
>
> db_args       = -adaptor DBI::mysql
>                -dsn mydb:myhost
>                -namespace volvox
>                -user me
>                -pass secret
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