Different organisms with same landmark IDs in gbrowse/chado

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Different organisms with same landmark IDs in gbrowse/chado

Olaf Mueller
Hi,
I setup a small test chado/postgres database with two organisms (yeast
and fission yeast). The data was uploaded via gmod_bulk_load_gff3.pl and
I curated and validated the gff3 files online before loading them. When
I try to access each genome via gbrowse I get an error message "Can't
call method "length" on an undefined value". The reason for this appears
to be that the landmark sequences (chromosomes) are named identically in
both organisms (chrI, chrII,...,etc.).

A small select query in chado:

         SELECT chromosome.feature_id, chromosome.uniquename,
chromosome.name
         FROM feature chromosome
         JOIN cvterm c ON chromosome.type_id = c.cvterm_id
         WHERE c.name = 'chromosome';

Shows this:

feature_id | uniquename |  name
------------+------------+---------
          15 | chrII      | chrII
          12 | chrIV      | chrIV
           8 | chrV       | chrV
          19 | chrVI      | chrVI
           4 | chrVII     | chrVII
           9 | chrIX      | chrIX
           7 | chrX       | chrX
          13 | chrXI      | chrXI
           5 | chrXII     | chrXII
          10 | chrXIV     | chrXIV
          11 | chrXV      | chrXV
          16 | chrXVI     | chrXVI
          17 | chrI       | chrI
          18 | chrIII     | chrIII
           3 | chrVIII    | chrVIII
          14 | chrXIII    | chrXIII
           6 | chrMito    | chrMito
       27271 | chrII      | chrII
       27270 | chrIII     | chrIII
       27269 | chrI       | chrI


The problem only occurs with the first three chromosomes since fission
yeast has only three of them.  So chrX works fine except for the fact
that it is displayed for both organisms. Is there a way to configure the
conf files in a way that gbrowse only displays organism specific
landmarks and features?

Thanks
Olaf

--
-----------------------------------------------------
Olaf Mueller, PhD
Roy J. Carver Center for Comparative Genomics
University of Iowa
Department of Biology (319) 335 1083 office
303 Biology Building (319) 335 1069 FAX
Iowa City, IA 52242-1324


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Re: Different organisms with same landmark IDs in gbrowse/chado

Scott Cain
Hi Olaf,

There is an "-organism" db_arg that you can supply in the database
section of the GBrowse config file, so it can look like this:

db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=chado;host=localhost;port=5432
                -user cain
                -organism 'Saccharomyces cerevisiae'

Are you doing this and still having a problem?  If so, what version of
Chado and Bio::DB::Das::Chado are you using?

Scott


On Wed, May 19, 2010 at 8:10 PM, Olaf Mueller <[hidden email]> wrote:

> Hi,
> I setup a small test chado/postgres database with two organisms (yeast
> and fission yeast). The data was uploaded via gmod_bulk_load_gff3.pl and
> I curated and validated the gff3 files online before loading them. When
> I try to access each genome via gbrowse I get an error message "Can't
> call method "length" on an undefined value". The reason for this appears
> to be that the landmark sequences (chromosomes) are named identically in
> both organisms (chrI, chrII,...,etc.).
>
> A small select query in chado:
>
>         SELECT chromosome.feature_id, chromosome.uniquename,
> chromosome.name
>         FROM feature chromosome
>         JOIN cvterm c ON chromosome.type_id = c.cvterm_id
>         WHERE c.name = 'chromosome';
>
> Shows this:
>
> feature_id | uniquename |  name
> ------------+------------+---------
>          15 | chrII      | chrII
>          12 | chrIV      | chrIV
>           8 | chrV       | chrV
>          19 | chrVI      | chrVI
>           4 | chrVII     | chrVII
>           9 | chrIX      | chrIX
>           7 | chrX       | chrX
>          13 | chrXI      | chrXI
>           5 | chrXII     | chrXII
>          10 | chrXIV     | chrXIV
>          11 | chrXV      | chrXV
>          16 | chrXVI     | chrXVI
>          17 | chrI       | chrI
>          18 | chrIII     | chrIII
>           3 | chrVIII    | chrVIII
>          14 | chrXIII    | chrXIII
>           6 | chrMito    | chrMito
>       27271 | chrII      | chrII
>       27270 | chrIII     | chrIII
>       27269 | chrI       | chrI
>
>
> The problem only occurs with the first three chromosomes since fission
> yeast has only three of them.  So chrX works fine except for the fact
> that it is displayed for both organisms. Is there a way to configure the
> conf files in a way that gbrowse only displays organism specific
> landmarks and features?
>
> Thanks
> Olaf
>
> --
> -----------------------------------------------------
> Olaf Mueller, PhD
> Roy J. Carver Center for Comparative Genomics
> University of Iowa
> Department of Biology           (319) 335 1083 office
> 303 Biology Building            (319) 335 1069 FAX
> Iowa City, IA 52242-1324
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Different organisms with same landmark IDs in gbrowse/chado

Olaf Mueller
Hi Scott,
many thanks, that worked instantly. So it doesn't matter if there are
identical uniquenames for a certain feature class within chado?

Olaf

> Hi Olaf,
>
> There is an "-organism" db_arg that you can supply in the database
> section of the GBrowse config file, so it can look like this:
>
> db_adaptor    = Bio::DB::Das::Chado
> db_args       = -dsn dbi:Pg:dbname=chado;host=localhost;port=5432
>                  -user cain
>                  -organism 'Saccharomyces cerevisiae'
>
> Are you doing this and still having a problem?  If so, what version of
> Chado and Bio::DB::Das::Chado are you using?
>
> Scott
>
>
> On Wed, May 19, 2010 at 8:10 PM, Olaf Mueller<[hidden email]>  wrote:
>    
>> Hi,
>> I setup a small test chado/postgres database with two organisms (yeast
>> and fission yeast). The data was uploaded via gmod_bulk_load_gff3.pl and
>> I curated and validated the gff3 files online before loading them. When
>> I try to access each genome via gbrowse I get an error message "Can't
>> call method "length" on an undefined value". The reason for this appears
>> to be that the landmark sequences (chromosomes) are named identically in
>> both organisms (chrI, chrII,...,etc.).
>>
>> A small select query in chado:
>>
>>          SELECT chromosome.feature_id, chromosome.uniquename,
>> chromosome.name
>>          FROM feature chromosome
>>          JOIN cvterm c ON chromosome.type_id = c.cvterm_id
>>          WHERE c.name = 'chromosome';
>>
>> Shows this:
>>
>> feature_id | uniquename |  name
>> ------------+------------+---------
>>           15 | chrII      | chrII
>>           12 | chrIV      | chrIV
>>            8 | chrV       | chrV
>>           19 | chrVI      | chrVI
>>            4 | chrVII     | chrVII
>>            9 | chrIX      | chrIX
>>            7 | chrX       | chrX
>>           13 | chrXI      | chrXI
>>            5 | chrXII     | chrXII
>>           10 | chrXIV     | chrXIV
>>           11 | chrXV      | chrXV
>>           16 | chrXVI     | chrXVI
>>           17 | chrI       | chrI
>>           18 | chrIII     | chrIII
>>            3 | chrVIII    | chrVIII
>>           14 | chrXIII    | chrXIII
>>            6 | chrMito    | chrMito
>>        27271 | chrII      | chrII
>>        27270 | chrIII     | chrIII
>>        27269 | chrI       | chrI
>>
>>
>> The problem only occurs with the first three chromosomes since fission
>> yeast has only three of them.  So chrX works fine except for the fact
>> that it is displayed for both organisms. Is there a way to configure the
>> conf files in a way that gbrowse only displays organism specific
>> landmarks and features?
>>
>> Thanks
>> Olaf
>>
>> --
>> -----------------------------------------------------
>> Olaf Mueller, PhD
>> Roy J. Carver Center for Comparative Genomics
>> University of Iowa
>> Department of Biology           (319) 335 1083 office
>> 303 Biology Building            (319) 335 1069 FAX
>> Iowa City, IA 52242-1324
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>      
>
>
>    


--
-----------------------------------------------------
Olaf Mueller, PhD
Roy J. Carver Center for Comparative Genomics
University of Iowa
Department of Biology (319) 335 1083 office
303 Biology Building (319) 335 1069 FAX
Iowa City, IA 52242-1324


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Re: Different organisms with same landmark IDs in gbrowse/chado

Scott Cain
Hi Olaf,

Good question: no, it doesn't.  The unique constraint on the feature
table is that the combination of uniquename, organism_id, and type_id
need to be unique.  So you can have a "ChrI" for each of your
organisms.

Scott


On Wed, May 19, 2010 at 11:20 PM, Olaf Mueller <[hidden email]> wrote:

> Hi Scott,
> many thanks, that worked instantly. So it doesn't matter if there are
> identical uniquenames for a certain feature class within chado?
>
> Olaf
>
>> Hi Olaf,
>>
>> There is an "-organism" db_arg that you can supply in the database
>> section of the GBrowse config file, so it can look like this:
>>
>> db_adaptor    = Bio::DB::Das::Chado
>> db_args       = -dsn dbi:Pg:dbname=chado;host=localhost;port=5432
>>                 -user cain
>>                 -organism 'Saccharomyces cerevisiae'
>>
>> Are you doing this and still having a problem?  If so, what version of
>> Chado and Bio::DB::Das::Chado are you using?
>>
>> Scott
>>
>>
>> On Wed, May 19, 2010 at 8:10 PM, Olaf Mueller<[hidden email]>
>>  wrote:
>>
>>>
>>> Hi,
>>> I setup a small test chado/postgres database with two organisms (yeast
>>> and fission yeast). The data was uploaded via gmod_bulk_load_gff3.pl and
>>> I curated and validated the gff3 files online before loading them. When
>>> I try to access each genome via gbrowse I get an error message "Can't
>>> call method "length" on an undefined value". The reason for this appears
>>> to be that the landmark sequences (chromosomes) are named identically in
>>> both organisms (chrI, chrII,...,etc.).
>>>
>>> A small select query in chado:
>>>
>>>         SELECT chromosome.feature_id, chromosome.uniquename,
>>> chromosome.name
>>>         FROM feature chromosome
>>>         JOIN cvterm c ON chromosome.type_id = c.cvterm_id
>>>         WHERE c.name = 'chromosome';
>>>
>>> Shows this:
>>>
>>> feature_id | uniquename |  name
>>> ------------+------------+---------
>>>          15 | chrII      | chrII
>>>          12 | chrIV      | chrIV
>>>           8 | chrV       | chrV
>>>          19 | chrVI      | chrVI
>>>           4 | chrVII     | chrVII
>>>           9 | chrIX      | chrIX
>>>           7 | chrX       | chrX
>>>          13 | chrXI      | chrXI
>>>           5 | chrXII     | chrXII
>>>          10 | chrXIV     | chrXIV
>>>          11 | chrXV      | chrXV
>>>          16 | chrXVI     | chrXVI
>>>          17 | chrI       | chrI
>>>          18 | chrIII     | chrIII
>>>           3 | chrVIII    | chrVIII
>>>          14 | chrXIII    | chrXIII
>>>           6 | chrMito    | chrMito
>>>       27271 | chrII      | chrII
>>>       27270 | chrIII     | chrIII
>>>       27269 | chrI       | chrI
>>>
>>>
>>> The problem only occurs with the first three chromosomes since fission
>>> yeast has only three of them.  So chrX works fine except for the fact
>>> that it is displayed for both organisms. Is there a way to configure the
>>> conf files in a way that gbrowse only displays organism specific
>>> landmarks and features?
>>>
>>> Thanks
>>> Olaf
>>>
>>> --
>>> -----------------------------------------------------
>>> Olaf Mueller, PhD
>>> Roy J. Carver Center for Comparative Genomics
>>> University of Iowa
>>> Department of Biology           (319) 335 1083 office
>>> 303 Biology Building            (319) 335 1069 FAX
>>> Iowa City, IA 52242-1324
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>
>>
>>
>
>
> --
> -----------------------------------------------------
> Olaf Mueller, PhD
> Roy J. Carver Center for Comparative Genomics
> University of Iowa
> Department of Biology           (319) 335 1083 office
> 303 Biology Building            (319) 335 1069 FAX
> Iowa City, IA 52242-1324
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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