[Bioperl-l] Living on the edg with 1.5?

[Phillip San Miguel]

    Because GBROWSE wants bioperl v 1.5 I'm moved to that on most of the 
platforms I use. But I've noticed two (presumably) unrelated glitches 
just in using it today. Should I really be using v 1.4? I'm not a 
developer, and don't really welcome additional headaches. Advice?

    Here are the bugs:

perl -e 'use Bio::Perl; $seq_object = get_sequence("genbank","u11059"); 
write_sequence(">test","genbank",$seq_object);'


fetches U11059 from genbank and tries to print in genbank format but 
something is wrong in v 1.5.

Running Version 1.5:

...
FEATURES             Location/Qualifiers
     source          1..7313
                     /mol_type="Bio::Annotation::SimpleValue=HASH(0x9b3870)"
                     
/tissue_type="Bio::Annotation::SimpleValue=HASH(0x9b38b8)"
                     /db_xref="Bio::Annotation::SimpleValue=HASH(0x9b3828)"
                     
/transposon="Bio::Annotation::SimpleValue=HASH(0x9b0968)"
                     /strain="Bio::Annotation::SimpleValue=HASH(0x9b3900)"
                     
/chromosome="Bio::Annotation::SimpleValue=HASH(0x9b3948)"
                     /organism="Bio::Annotation::SimpleValue=HASH(0x9b3990)"
     LTR             1..649
                     /label=Bio::Annotation::SimpleValue=HASH(0x9aefd4)
     TATA_signal     304..310
                     /label=Bio::Annotation::SimpleValue=HASH(0x9b55fc)
     misc_feature    651..659
                     /label=Bio::Annotation::SimpleValue=HASH(0x9b5764)
...

Running Version 1.4 (no problem):

...
FEATURES             Location/Qualifiers
     source          1..7313
                     /transposon="retrotransposon"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:4577"
                     /tissue_type="leaf"
                     /strain="A188"
                     /chromosome="7"
                     /organism="Zea mays"
     LTR             1..649
                     /label=upstreamLTR
     TATA_signal     304..310
                     /label=upstream
     misc_feature    651..659
                     /label=PBSsite
...

The other 1.5 bug I found today: The following one-liner demonstrates it:

perl -e 'use Bio::SeqIO;use Bio::Seq::PrimaryQual; $qual_object = 
Bio::Seq::PrimaryQual->new(-qual=> "10 20 30 40 50 40 30 20 10", -id => 
"test", -format => 'qual'); $qual_out = Bio::SeqIO->new(-file => 
">test", -format => 'qual');$qual_out->write_seq($qual_object);'

When I run it under Version 1.5 the correct output file is produced but 
I also get the following output sent to STDOUT:

'_root_verbose' => 0
'display_id' => 'test'
'qual' => ARRAY(0x5b07e8)
   0  10
   1  20
   2  30
   3  40
   4  50
   5  40
   6  30
   7  20
   8  10

Under Version 1.4 everything is fine. (No extraneous STDOUT is created.)

This looks like someone uncommented a Data::Dumper print somewhere, but 
I wasn't able to find it.

-- 
Phillip SanMiguel
Purdue Genomics Core Facility