Parent/parent_id attribute

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Parent/parent_id attribute

Daniel Lang-3
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:     [hidden email]

#################################################
My software never has bugs.
It just develops random features.
#################################################



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Re: 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 <[hidden email]> 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:     [hidden email]
>
> #################################################
> My software never has bugs.
> It just develops random features.
> #################################################
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: Parent/parent_id attribute

Daniel Lang-3
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 <[hidden email]> 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:     [hidden email]
>>
>> #################################################
>> My software never has bugs.
>> It just develops random features.
>> #################################################
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>





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Re: 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 <[hidden email]> 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 <[hidden email]> 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:     [hidden email]
>>>
>>> #################################################
>>> My software never has bugs.
>>> It just develops random features.
>>> #################################################
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
>
>


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