Re: [Gmod-gbrowse] APOLLO match/match_part problem

[Joelle Amselem]

Dear Alessandro,

The apollo list is in cc

In your chado DB
> analysis_id program programversion sourcename
> 55 SWISSPROT null NULL

        analysis.sourcename=NULL
        analysis.program=SWISSPROT

In yourfile.tiers
> resulttype : SWISSPROT:SWISSPROT
it should be
        resulttype : analysis.program:analysis.sourcename
so in your case
        resulttype : SWISSPROT:NULL

I am not sure that "NULL"  will work.
the analysis.sourcename could be something as "genome_vs_SWISSPROT"
the analysis.program could be "blastx" opr "blastp" ....
the analysis.name could be "blastx_SWISSPROT"

Note also that in chado there is a unicity constraint on (program, programversion, sourcename)

Hope it will works !
Joelle
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Joelle Amselem
INRA-URGI
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Le 22 juil. 2011 à 16:01, alessandroalbiero a écrit :

> Dear all,
>
> I'm posting here even if I'm not sure that this is the Apollo Mailing List
> (if not, please let me know where I can post... :-) )
> I'm setting Apollo and a CHADO database. At the moment when I start Apollo I
> can see only the gene prediction tracks but I'm not able to charge the
> alignment tracks.
>
> I uploaded all the aligment tracks with gmod_bulk_load_gff3.pl script using
> --analysis option and the GFFs have this structure:
>
> chr1    SWISSPROT       match   19607557        19610788        .       -      
> .      ID=1_SWISSPROT_1;Name=A2XUW1_CDKG2_ORYSI.316483;
> chr1    SWISSPROT       match_part      19607557        19607620        .      
> -       .      
> ID=1_SWISSPROT_1_1;Name=A2XUW1_CDKG2_ORYSI.316483;Note=sim:100;Parent=1_SWISSPROT_1
> chr1    SWISSPROT       match_part      19607724        19607830        .      
> -       .      
> ID=1_SWISSPROT_1_2;Name=A2XUW1_CDKG2_ORYSI.316483;Note=sim:100;Parent=1_SWISSPROT_1
>
> I checked and  SWISSPROT (with other programs) is present in the analysis
> table:
> analysis_id program programversion sourcename
> 55 SWISSPROT null NULL
>
> I tried to add "SWISSPROT" in the chado-adapter.xml file both in
> <genePredictionPrograms> and in <searchHitPrograms>
> and I also used this tier:
>
> [Tier]
> tiername : Alignment
> expanded : false
> labeled : false
> visible : true
>
> [Type]
> tiername : Alignment
> typename : SWISSPROT:SWISSPROT
> resulttype : SWISSPROT:SWISSPROT
> color : 0,255,0
> usescore : true
> minscore : 0
> maxscore 100
> glyph : DrawableResultFeatureSet
> column : NAME
> column : SCORE
> column : GENOMIC_RANGE
> column : MATCH_RANGE
> column : GENOMIC_LENGTH
> column : MATCH_LENGTH
> sortbycolumn : GENOMIC_RANGE
> groupby : HOMOLOGY
>
>
> At the moment I have never charged this track.... I do not have any idea...
> Can someone, please, help me ?
>
> All the best
>
> Alessandro Albiero
>
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/APOLLO-match-match-part-problem-tp4623165p4623165.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
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