Hi Rohit I tried loading that example but with the noexon flag as the output you sent suggested but it complains about YAL069W not having a parent. As you do not get any rows with the query I sent I suspect it has not loaded properly and it is not finding the chromosome feature.
For an example with Artemis have a look at this tutorial: http://www.sanger.ac.uk/Software/Artemis/v11/chado/GMOD2009SummerSchool.shtm l#Examples_of_Loading_Sequences_into_the_Database The query I sent you searches the feature table for entries that have residues for Artemis to open up (e.g. chromosome, contig features). Regards Tim On 10/26/09 7:28 PM, "parimi rohit" <rohit.par...@gmail.com> wrote: > Hi Tim, > > Thanks for your quick response. I tried to create a new chado database and > load the example data available in the wiki tutorial in to it. > http://gmod.org/wiki/Load_GFF_Into_Chado . I created the database, used the > gmod_bulk_load_gff.pl <http://gmod_bulk_load_gff.pl> script to load yeast > data into the database. > > This is the terminal output display what i got: > > [r...@agron-90-78 Chadotesting]# gmod_bulk_load_gff3.pl > <http://gmod_bulk_load_gff3.pl> --gfffile saccharomyces_cerevisiae.gff.sorted > --organism yeast --dbname rohit_chado_01 --dbuser rohit --dbpass redearth > -dbhost localhost --recreate_cache > (Re)creating the uniquename cache in the database... > Creating table... > Populating table... > Creating indexes...Done. > Preparing data for inserting into the rohit_chado_01 database > (This may take a while ...) > > This file was not declared as analysis results (with the --analysis flag, > but this file contains attributes that imply that it is: > * Has a match feature type > You can safely ignore this message if you don't need to access scores > associated with these features. > > This GFF file has CDS and/or UTR features that do not belong to a > 'central dogma' gene (ie, gene/transcript/CDS). The features of > this type are being stored in the database as is. > > There are both CDS and exon features in this file, but > you did not set the --noexon option, which you probably want. > Please see `perldoc gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> > for more information. > > Loading data into feature table ... > Loading data into featureloc table ... > Loading data into feature_relationship table ... > Loading data into featureprop table ... > Loading data into feature_cvterm table ... > Loading data into synonym table ... > Loading data into feature_synonym table ... > Loading data into dbxref table ... > Loading data into feature_dbxref table ... > Skipping analysisfeature table since the load file is empty... > Loading data into cvterm table ... > Loading data into db table ... > Skipping cv table since the load file is empty... > Skipping analysis table since the load file is empty... > Skipping organism table since the load file is empty... > Adding cvtermprop=MapReferenceType for 'chromosome' ... > Adding cvtermprop=MapReferenceType to chromosome ... > Loading sequences (if any) ... > Optimizing database (this may take a while) ... > (feature featureloc feature_relationship featureprop feature_cvterm synonym > feature_synonym dbxref feature_dbxref analysisfeature cvterm db cv analysis > organism ) Done. > > While this script has made an effort to optimize the database, you > should probably also run VACUUM FULL ANALYZE on the database as well > > I think the data is loaded into the tables as I tested for one of the table. > > I tried the query that you wrote to me in your previous mail and it fetched 0 > rows. I do not know why it is not fetching the any data. I am relatively new > to this field and do not know what the data is and how to analyze the data. I > have no idea of what you meant by "This assumes that the sequence features > have type_id *chromosome*, *sequence*, supercontig, ultra_scaffold, > golden_path_region or contig. If your sequence features do not belong to that > list you can modify it in artemis_sqlmap/Feature.xml. Please let me know if > you think something needs adding to this list." . I could understand that it > is trying to fetch some data which is not available in the database. Can you > please help me understand how this works and how to modify for the data I > loaded in to the database. This data is available in the wiki link that I gave > above and is of the organism "Yeast". > > I really appreciate your help. > > Thanks and Regards, > Rohit > > > > > > On Thu, Oct 22, 2009 at 3:11 PM, Tim Carver <t...@sanger.ac.uk> wrote: >> Hi Rohit >> >> The first error suggests a strange character in your cvterm table in the >> column is_relationshiptype. There appears to be a charcter (t?) when the >> mapping is expecting an integer. You should find that and change it to an >> integer. >> >> The second exception looks like it has failed to find the sequences. To find >> the organisms with top level features with residues it runs this query which >> you can try : >> >> SELECT DISTINCT ON( feature.organism_id ) >> organism.organism_id AS organismId, >> abbreviation, genus, species, common_name AS commonName, comment >> FROM feature >> join organism using (organism_id) >> join cvterm on feature.type_id = cvterm.cvterm_id >> WHERE residues notnull AND residues != '' >> AND (cvterm.name <http://cvterm.name> LIKE '%chromosome%' OR cvterm.name >> <http://cvterm.name> LIKE '%sequence%' OR >> cvterm.name <http://cvterm.name> IN ('supercontig', 'ultra_scaffold', >> 'golden_path_region', 'contig')); >> >> This assumes that the sequence features have type_id *chromosome*, >> *sequence*, supercontig, ultra_scaffold, golden_path_region or contig. If >> your sequence features do not belong to that list you can modify it in >> artemis_sqlmap/Feature.xml. Please let me know if you think something needs >> adding to this list. >> >> Regards >> Tim >> >> >> On Thu, 22 Oct 2009, parimi rohit wrote: >> >>> Hi All, >>> >>> I am following the wiki page that has the tutorial to integrate Artemis with >>> Chado schema. I have >>> postgres as well as chado schema installed. I used Apollo to annotate data >>> from one of the >>> databases that we created. Now, I am trying to use Artemis on the same data. >>> However I am having >>> problems in running Artemis over the database. I started Artemis with the >>> following command as >>> given in the wiki page: >>> >>> $: ./art -Dchado="localhost:5432/rohit_chado_01?rohit" -Dibatis >>> >>> I entered my credentials in the login window and the Database and File >>> Manager window opened. >>> However I am able to view nothing in the Database part of the window even >>> though there exist >>> many. Also double clicking the folder in the database window is giving an >>> exception in the >>> terminal. >>> >>> I copied the terminal errors in a text file and I am attaching it in this >>> mail. The attachment >>> contains error information for 2 different databases. Please let me know the >>> problem and the way >>> to solve this so that it will work with the data that we have. >>> >>> Regards, >>> Rohit >>> >>> >>> >>> >>> >> _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
