setting GBrowse database and query GFF3

[firozsiwan]

(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

[emanlee]

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

[firozsiwan]

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

Thanks

[emanlee]

REF:

http://generic-model-organism-system-database.450254.n5.nabble.com/Getting-gbrowse-syn-to-work-with-MySQL-td5519255.html

[kmcarr]

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?)