Hi Joelle, Could you perhaps provide me with "SELECT" access to the database (or a dump of the database with the mentioned data)? I'll need to inspect how the data is stored to figure out what's going on. Did you use the GFF3 bulk loader to populate the Chado instance? If so, I have a feeling there might be some issue with using "match_set". This SO term is obsolete so maybe this is causing an issue somehow. You should be using "match" instead.
Cheers, Ed On Fri, 2008-11-21 at 08:36 +0100, Joëlle Amselem wrote: > Hello, > > > I'm running an apollo 1.9.6 connected to a chado database and having > trouble with match_set connected because they share the same target. > > > But we can see on the gff below that they are 2 different Match_set, > each one parent of 2 match_part. > In gbrowse the display is OK : 2 match_part with the same parent are > connected but the 2 match_set are not. > > > Is there another way (with other type of feature than > math_set/match_part) to store data in chado to avoid this. > > > > > bt4ctg_0009 blastx_uniprot_sprot match_set 22244 23492 > 1e-160 - . > ID=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039;Target=uniprot_sprot|Q9HFQ2|PP2A1_EMENI+1 > +323;Name=bt4ctg_0009_uniprot_sprot|Q9HFQ2|PP2A1_EMENI > bt4ctg_0009 blastx_uniprot_sprot match_part 22244 23017 > 1e-160 - 1 > ID=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039_match_part0001;Target=uniprot_sprot|Q9HFQ2| > PP2A1_EMENI+100 > +323;Parent=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039 > bt4ctg_0009 blastx_uniprot_sprot match_part 23058 23492 > 1e-160 - . > ID=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039_match_part0003;Target=uniprot_sprot|Q9HFQ2| > PP2A1_EMENI+1 > +104;Parent=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039 > ### > bt4ctg_0009 blastx_uniprot_sprot match_set 89534 90523 > 1e-160 - . > ID=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039bis;Target=uniprot_sprot|Q9HFQ2|PP2A1_EMENI+1 > +323;Name=bt4ctg_0009_uniprot_sprot|Q9HFQ2|PP2A1_EMENI > bt4ctg_0009 blastx_uniprot_sprot match_part 89970 90248 > 4e-91 - . > ID=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039_match_part0002;Target=uniprot_sprot|Q9HFQ2| > PP2A1_EMENI+101 > +193;Parent=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039bis > bt4ctg_0009 blastx_uniprot_sprot match_part 90299 90523 > 4e-91 - 1 > ID=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039_match_part0005;Target=uniprot_sprot|Q9HFQ2| > PP2A1_EMENI+30 > +104;Parent=blastx_uniprot_sprot_bt4ctg_0009_uniprot_sprot|Q9HFQ2| > PP2A1_EMENI_match_set0039bis > > > Thanks in advance > Joelle > ----------------------------------------------------------------- > Joelle Amselem > INRA - URGI/BIOGER > Route de Saint-Cyr 78026 Versailles cedex > tel: +33 1 30 83 33 95 > > ----------------------------------------------------------------- > > > _______________________________________________ > apollo mailing list > [email protected] > http://mail.fruitfly.org/mailman/listinfo/apollo _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
