[Bioperl-l] Parent/parent_id attribute

[Daniel Lang]

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

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It just develops random features.
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