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

[Hilmar Lapp]

Don't use 1.5.0 for now. It's SeqFeatureI is broken and isn't nor ever 
was ready for release. Sorry about this glitch.

	-hilmar

On Thursday, March 10, 2005, at 02:35  PM, Phillip San Miguel wrote:

>
>    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
>
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>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------