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  • setting GBrowse database and query GFF3

    (1) I have uploaded the genome fasta and GFF annotation in the mysql data using following command of Bio:B::SeqFeature::Store database

    ./bp_seqfeature_load.pl -c -d WS240 -u xxx -p xxx c_elegans.PRJNA13758.WS240.genomic.fa c_elegans.PRJNA13758.WS240.annotations.gff3

    (2) Following tables are inserted into my database WS240
    +-----------------+
    | Tables_in_WS240 |
    +-----------------+
    | attribute |
    | attributelist |
    | feature |
    | locationlist |
    | meta |
    | name |
    | parent2child |
    | sequence |
    | typelist |
    +-----------------+

    (3) Now I want to make query in the mysql to extract the sequence and its feature using following commands:

    #!/usr/bin/perl
    use strict;


    use Bio:B::GFF;

    my $db = Bio:B::GFF->new(-dsn => 'dbi:mysql:database=WS240',
    -user => 'XXX',
    -pass => 'XXX',
    -aggregators => 'gene_model{coding_exon,5_UTR,3_UTR/CDS}');

    my $gene_stream = $db->get_seq_stream('gene_model:curated');

    while (my $gene = $gene_stream->next_seq) {
    print $gene->name,"\n";
    for my $part ($gene->get_SeqFeatures) {
    print "\t",join("\t",$part->method,$part->start,$part->end),"\n";
    }
    print "\n";
    }



    (4) I am getting following error:
    ------------- EXCEPTION: Bio::Root::Exception -------------
    MSG: Couldn't execute query SELECT fref,fstart,fstop,fsource,fmethod,fscore,fstrand,fphase,gclass,gname,ftarget_start,ftarget_stop,fdata.fid,fdata.gid
    FROM fdata,ftype,fgroup
    WHERE fgroup.gid = fdata.gid
    AND ftype.ftypeid = fdata.ftypeid
    AND ((fmethod = ? AND fsource = ?) OR (fmethod = ? AND fsource = ?) OR (fmethod = ? AND fsource = ?) OR (fmethod = ? AND fsource = ?))
    ORDER BY fgroup.gname:
    Table 'WS240.fdata' doesn't exist

    STACK: Error::throw
    STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
    STACK: Bio:B::GFF::Adaptor::dbi::caching_handle::do_query /usr/local/share/perl/5.10.0/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:123
    STACK: Bio:B::GFF::Adaptor::dbi::range_query /usr/local/share/perl/5.10.0/Bio/DB/GFF/Adaptor/dbi.pm:627
    STACK: Bio:B::GFF::Adaptor::dbi::get_features_iterator /usr/local/share/perl/5.10.0/Bio/DB/GFF/Adaptor/dbi.pm:1008
    STACK: Bio:B::GFF::_features /usr/local/share/perl/5.10.0/Bio/DB/GFF.pm:3476
    STACK: Bio:B::GFF::features /usr/local/share/perl/5.10.0/Bio/DB/GFF.pm:1091
    STACK: Bio:B::GFF::get_seq_stream /usr/local/share/perl/5.10.0/Bio/DB/GFF.pm:1132
    STACK: ./aa.pl:12


    (5) Could you kindly suggest me what is wrong with the script (3), what is the best approach to make query with mysql. I also used the bp_bulk_load_gff.pl (Bio:B::GFF) to upload the GFF file into mysql but not working well.

    Thanks

  • #2
    What is between "use Bio:" and "B::GFF;" in the perl script "use Bio: icon B::GFF;" ?

    Comment


    • #3
      sorry, it was automatic converted into symbol. it is Bio then :: then DB then :: then GFF
      so "icon" is ":"D

      Thanks
      Last edited by firozsiwan; 05-19-2014, 03:18 PM.

      Comment


      • #5
        You created a Bio:B::SeqFeature database but then are trying to query it with the Bio:B::GFF adapter. This won't work because the database schemas are entirely different. Build your script to use Bio:B::SeqFeature adapter to query the database.

        BTW Bio:B::GFF is deprecated in favor of Bio:B::SeqFeature.

        (How many grins was that?)

        Comment

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