[Bioperl-l] Parent/parent_id attribute

[Fields, Christopher J]

Hi Daniel,

Not sure if you got an answer to this one yet.  I’m cc’ing the gmod-gbrowse group just in case this was missed here.  

chris

On Sep 22, 2014, at 1:13 PM, Daniel Lang <Daniel.Lang at biologie.uni-freiburg.de> wrote:

> Hi,
> 
> I'm using bioperl 1.6.923-1 (Ubuntu Trusty package) and
> Bio::DB::SeqFeature to store and manipulate GFF3 files.
> 
> I'm wondering why the "Parent" GFF3 attributes are stored as parent_id
> values in the feature objects, but not returned as such in the gff3_string?
> 
> GFF3:
> Chr01   transdecoder    mRNA    5216    5627    .       +       .
> ID=T1.Chr01.mRNA.1;Parent=T1.Chr01.gene.1;Alias=T1.asmbl_1|m.6484,T1.ORF;Name=T1.Chr01.mRNA.1
> 
> Example debugger trace after fetching stored feature:
> 
> x $f
> 0  Bio::DB::SeqFeature=HASH(0x3e3a798)
>   'attributes' => HASH(0x3e3a858)
>      'Alias' => ARRAY(0x3e3a8b8)
>         0  'T1.asmbl_1|m.6484'
>         1  'T1.ORF'
>      'load_id' => ARRAY(0x3e3aca8)
>         0  'T1.Chr01.mRNA.1'
>      'parent_id' => ARRAY(0x3e3acf0)
>         0  'T1.Chr01.gene.1'
>   'is_circular' => 0
>   'name' => 'T1.Chr01.mRNA.1'
>   'phase' => undef
>   'primary_id' => 2428
>   'ref' => 'Chr01'
>   'score' => undef
>   'source' => 'transdecoder'
>   'start' => 5216
>   'stop' => 5627
>   'store' => Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x39b95d0)
>      'class_loaded' => HASH(0x3e3a2b8)
>         'Bio::DB::SeqFeature' => 1
>      'dbh' => DBI::db=HASH(0x3dc1e40)
>           empty hash
>      'dumpdir' => '/tmp'
>      'is_temp' => undef
>      'namespace' => undef
>      'seqfeatureclass' => 'Bio::DB::SeqFeature'
>      'settings_cache' => HASH(0x3dc1d98)
>         'autoindex' => 1
>         'compress' => 0
>         'index_subfeatures' => 1
>         'serializer' => 'Storable'
>      'writeable' => undef
>   'strand' => 1
>   'type' => 'mRNA'
> 
> x $f->gff3_string
> 0
> "Chr01\cItransdecoder\cImRNA\cI5216\cI5627\cI.\cI+\cI.\cIName=T1.Chr01.mRNA.1;ID=2428;Alias=T1.asmbl_1%7Cm.6484,T1.ORF"
> 
> What is the best practice to store parentage? I'm currently adding an
> additional "Parent" value using add_tag_value.
> 
> Or is this a bug in the version I'm using?
> 
> Best,
> Daniel
> -- 
> 
> Dr. Daniel Lang
> University of Freiburg, Plant Biotechnology
> Schaenzlestr. 1, D-79104 Freiburg
> fax:        +49 761 203 6945
> phone:      +49 761 203 6989
> homepage:   http://www.plant-biotech.net/
>            http://www.cosmoss.org/
> e-mail:     daniel.lang at biologie.uni-freiburg.de
> 
> #################################################
> My software never has bugs.
> It just develops random features.
> #################################################
> 
> 
> 
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