#7 please help with generate_histogram.pl

[Yair Benita]

I have applied the Generic Genome Browser to my own database
and everything appears to be working great. The only thing I am
having problems with is the generate_histogram script.

Here is an example of my original gff file before it was loaded to
mysql:

Chr22    HumanEST    full_length_est    40787080    40787317   
.    +     .    EST "AI741058"
Chr22    HumanEST    est_fragment    44479404    44479467    .   
+    .    EST "BX454516"

The ESTs are aggregated as follows in the conf file:
EST{est_fragment/full_length_est}

To generate the density data I used:
 generate_histogram.pl -merge -d 4d_chr22 -u me -p myPass -bin
5000 EST >est_density.gff

It fails also when I use an other feature. Here is the error
message:

------------- EXCEPTION  -------------

MSG: Couldn't execute query SELECT  fref,

1+10000*floor(fstart/10000)   as fstart,

10000*(1+floor(fstart/10000)) as fstop,

IF(ISNULL(fsource),fmethod,concat(fmethod,':',fsource)),'bin',

count(*) as fscore,

'.','.','bin',

IF(ISNULL(fsource),concat(fref,':',fmethod),concat(fref,':',fmethod,'

:',fsource)),

NULL,NULL,NULL,NULL

FROM fdata,ftype,fgroup

WHERE   fgroup.gid = fdata.gid

AND ftype.ftypeid = fdata.ftypeid

AND  ((fmethod = ?))

Mixing of GROUP columns (MIN(),MAX(),COUNT()...) with no
GROUP columns is illegal if there is no GROUP BY clause

STACK Bio::DB::GFF::Adaptor::dbi::caching_handle::do_query /
Library/Perl/5.8.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:128

STACK Bio::DB::GFF::Adaptor::dbi::range_query /Library/Perl/
5.8.1/Bio/DB/GFF/Adaptor/dbi.pm:636
STACK Bio::DB::GFF::Adaptor::dbi::get_features /Library/Perl/
5.8.1/Bio/DB/GFF/Adaptor/dbi.pm:313
STACK Bio::DB::GFF::_features /Library/Perl/5.8.1/Bio/DB/GFF.pm:
3111
STACK Bio::DB::GFF::features /Library/Perl/5.8.1/Bio/DB/GFF.pm:
924
STACK toplevel /usr/local/bin/generate_histogram.pl:53
------------------------------------------

I can't figure out the problem. It seems there is a problem in the
query but looking in the database it looks fine to me. What do you
think is wrong?

Thanks for any help you can give.

All the best,
Yair Benita

[Scott Cain]

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Yair,

This is a pretty old request--I'm guessing you sorted this
out, right?

Scott

[SourceForge Robot]

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