[Bioperl-l] Parent/parent_id attribute

[Daniel Lang]

Hi Chris,

thanks for you response! No, there hasn't been a response yet.

The solution with add_tag_value('Parent') works for me tough.

Best,
Daniel

On 28.09.2014 05:26, Fields, Christopher J wrote:
> 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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>