[Bioperl-l] Bio::DB::SeqFeature

Daniel Lang daniel.lang at biologie.uni-freiburg.de
Thu Oct 5 13:12:02 EDT 2006


Hi,

we are storing Bio::SeqFeature::Gene::GeneStructure objects (with
multiple transcripts) using Bio::DB::SeqFeature::Store in a mysql db
(latest bioperl-live checkout).

The Bio::SeqFeature::Gene::GeneStructure's are generated from scratch
out of a database.

The first observation is that is seems to work (fetched objects behave
like Bio::SeqFeature::Gene::GeneStructure's) despite the fact that we
get these warnings:

Can't store item CODE(0x113db10) at lib/Storable.pm (autosplit into
lib/auto/Storable/_freeze.al) line 287, <STDIN> line 1.
Can't store item CODE(0x11786f0) at lib/Storable.pm (autosplit into
lib/auto/Storable/_freeze.al) line 287, <STDIN> line 1.
        (in cleanup) Not a CODE reference at
/home/lang/bioperl/bioperl-live//Bio/Root/Root.pm line 438, <STDIN> line 1.
prepare_cached(SELECT f.id,f.object
  FROM feature as f
  WHERE (   f.seqid=?
   AND   f.end>=? AND f.start<=? AND ((f.tier=? AND f.bin between ? AND ?)
         OR (f.tier=? AND f.bin between ? AND ?)
         OR (f.tier=? AND f.bin between ? AND ?)
         OR (f.tier=? AND f.bin between ? AND ?)
         OR (f.tier=? AND f.bin between ? AND ?)
         OR (f.tier=? AND f.bin between ? AND ?)
         OR (f.tier=? AND f.bin between ? AND ?))
)

) statement handle DBI::st=HASH(0x1c317cf0) still Active at
/home/lang/bioperl/bioperl-live//Bio/DB/SeqFeature/Store/DBI/mysql.pm
line 1422
        (in cleanup) Not a CODE reference at
/home/lang/bioperl/bioperl-live//Bio/Root/Root.pm line 438, <STDIN> line 1.

Is this something serious? Does this mean that the stored object doesn't
have everything it had before freezing? Or are we using
Bio::DB::SeqFeature inappropriately?

The other question would be, if we can visualize these stored feature
objects easily using gbrowse? I didn't find a hint mentioning
Bio::DB::SeqFeature as being supported by gbrowse on the gmod pages...
Is it working already? Will it?

Thanks in advance,
Daniel

-- 

Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax: +49 761 203 6945
phone: +49 761 203 6974
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

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It just develops random features.
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