Works perfectly now...
Thanks Scott!
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-05-31, at 2:51 PM, Scott Cain wrote:

Ah, OK, now I see.

This is actually related to a problem Olen was just writing about over
the last few days.  Generally, I advise against having ID != Name for
srcfeatures (like chromosomes) to avoid just this sort of thing.  If
you must make them different, column 1 should agree with the Name, not
the ID.

Scott


On Tue, May 31, 2011 at 4:40 PM, Lacey-Anne Sanderson
<laceyanne_sanderson@shaw.ca> wrote:
Hi Scott,
Chad has created a tripal module that generates a GFF3 file from the
tripal/chado database. He then uses bp_seqfeature_load.pl to load that GFF3
file into a MySQL database specified by the user. He's running into problems
while loading that file...
For example,
His script creates the attached file (temporaryGBrowse_1306872204.gff3) and
then executes:
bp_seqfeature_load.pl -c -u 'dbadmin' -p 'password' -d testJune
/tmp/temporaryGBrowse_1306872204.gff3
loading /tmp/temporaryGBrowse_1306872204.gff3...
Building object tree... 0.00s

load time:  0.02s
No errors are produced... but then when you go to GBrowse in the
browser: http://knowpulse2.usask.ca/cgi-bin/gbrowse/testJune
and search for one of the features that were supposed to be loaded (ie:
Chr1) you get The landmark named Chr1 is not recognized. Similarly if you
search using the GFF3 ID (ie: Mt3.5.1Chr1).
When I saw this I thought: well we should check to see if it's in the
database so I checked the MySQL GBrowse database testJune and it seems to be
there:
mysql> select * from feature limit 1;
+----+--------+-------+-------+----------+--------+------+------+---------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| id | typeid | seqid | start | end      | strand | tier | bin  | indexed |
object


                                                           |
+----+--------+-------+-------+----------+--------+------+------+---------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  1 |      1 |     1 |     1 | 34297684 |      0 |    5 |    0 |       1 |
Bio::DB::SeqFeature
'Medicago Pseudomolecules (Assembly 3.5)   source
primary_id   store
34297684   stop
Mt3.5.1Chr1   re?
                    is_circular
Chr1   name   score   phas?   strand
chromosome   type
Mt3.5.1Chr1   load_id
attributes
1   start |
+----+--------+-------+-------+----------+--------+------+------+---------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
1 row in set (0.00 sec)

When we load in a completely different GFF3 (coded by hand not generated by
his program) using the same database and configuration file, it works...
Any idea what the problem is? His GFF3 looks fine to me...
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Email: laceyanne_sanderson@shaw.ca
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan
On 2011-05-31, at 2:27 PM, Krizbomb . wrote:


Date: Tue, 31 May 2011 15:23:34 -0400
From: scott@scottcain.net
Subject: Re: [Gmod-gbrowse] Problem Uploading a GFF3 File
To: cnk046@mail.usask.ca
CC: gmod-gbrowse@lists.sourceforge.net

Hi Chad,

Could you explain in more detail what should be happening? I'm
wondering because it sounds like you're expecting to find your data in
a Chado database after upload, but you're using bp_seqfeature_load.pl,
which loads data into a SeqFeature::Store database. Perhaps I don't
fully understand what is happening though. Also, I want to make sure
we are not talking about using the upload functionality built into
GBrowse, right?

Thanks,
Scott


On Tue, May 31, 2011 at 1:30 PM, Chad Krilow <cnk046@mail.usask.ca> wrote:
 Hello,


My name is Chad Krilow, I am a Bioinformatics research assistant working
with the University of Saskatchewan. I have developed a Drupal module
that provides an interface to register already existing GBrowse
instances
with Drupal/Tripal and/or create new GBrowse Instances. Furthermore, it
allows basic management of these GBrowse instances including
un-registering
and/or deleting and loading of features in Tripal/Chado into a MySQL
GBrowse
instance. As such, it provides interoperability
and synchronization between
a Tripal/Chado installation and GBrowse. Though when it comes to
uploading
the GFF3 file, which is attached, no errors are thrown by the script,
and
when we look in the database the features are in the feature table, but
when
we search through the GBrowse interface we "Landmark Not Found". We are
searching using the name from the GFF3 file, but the ID does not work
either. The loading script that we are using is as
follows: bp_seqfeature_load.pl. When we Load the feature into GBrowse
the
following is output:
tripal_gbrowse_load_features_into_gbrowse(chad_test, dbadmin,
<***PASSWORD***>, 61, 1, 471).  So my query is that is there a GBrowse
problem, a problem with the format of the GFF3 file being created? As we
ran
the same loading script, and a GFF3 file created by hand, and it loaded
correctly using the same database and configuration file. This should
rule
out the loading script and the configuration file being a source of the
problem. So any help that you could give me would be greatly
appreciated.
Cheers & Thanks,
Chad Krilow




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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research