[Bioperl-l] Parent/parent_id attribute

[Fields, Christopher J]

It’s been a little quiet lately :)

chris

On Oct 15, 2014, at 4:03 AM, Daniel Lang <Daniel.Lang at biologie.uni-freiburg.de> wrote:

> 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.
>>> #################################################
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
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