[BioC] Making use of the Apis mellifera assembly 2 data in goSeq

Tue Feb 28 20:04:01 CET 2012

Hi Vanessa,

Please let's keep this discussion on the list (I should have said use
the "Reply All" button instead of "Reply" in my previous email).

On 02/28/2012 07:57 AM, Corby, Vanessa wrote:
> Hello Hervé,
>
> So it looks like it made a .sqlite file called "org.Amellifera.eg.sqlite" in the specified directory, but I don't see an associated package.  I see in the AnnotationDbi information there is a wrapBaseDBPackages function.  Would this be the next step?

More importantly, it seems that you got an error (see below), which
would explain why the package is half-backed only.

>
> Here is my input into R and what I got out:
>
>> makeOrgPackageFromNCBI(version = "0.1", author = "Vanessa Corby-Harris<vanessa.corby at ars.usda.gov>", maintainer = "Vanessa Corby-Harris<vanessa.corby at ars.usda.gov>", outputDir = "/homeB/home4/u8/vlcorbyharris", tax_id = "7469", genus = "Apis",  species = "mellifera")
> Getting data for gene2pubmed.gz
> Populating gene2pubmed table:
> table gene2pubmed filled
> Getting data for gene2accession.gz
> Populating gene2accession table:
> table gene2accession filled
> Getting data for gene2refseq.gz
> Populating gene2refseq table:
> table gene2refseq filled
> Getting data for gene2unigene
> Populating gene2unigene table:
> table gene2unigene filled
> Getting data for gene_info.gz
> Populating gene_info table:
> table gene_info filled
> Getting data for gene2go.gz
> Populating gene2go table:
> Getting blast2GO data as a substitute for gene2go
> Error in file(file, "rt") : invalid 'description' argument
> In addition: Warning message:
> In unzip(tmp) : error 1 in extracting from zip file

I'm trying to reproduce this but makeOrgPackageFromNCBI() seems to take
a long time (started this 10+ minutes ago). In the mean time could you
please provide your sessionInfo()? This is an absolute requisite for us
to troubleshoot. Also make sure you read our posting guide:

   http://bioconductor.org/help/mailing-list/

Thanks,
H.

>
> Vanessa
> -----Original Message-----
> From: Hervé Pagès [mailto:hpages at fhcrc.org]
> Sent: Monday, February 27, 2012 3:14 PM
> To: Corby, Vanessa; bioconductor at r-project.org
> Subject: Re: [BioC] Making use of the Apis mellifera assembly 2 data in goSeq
>
> On 02/27/2012 02:02 PM, Corby, Vanessa wrote:
>> Argh.  This is what I was afraid of...
>
> Why not try to make yours? See the makeOrgPackageFromNCBI() function in
> AnnotationDbi:
>
>     library(AnnotationDbi)
>     ?makeOrgPackageFromNCBI
>
> (Would be nice if the goseq documentation could mention this.)
>
> If you run into problems while trying to use makeOrgPackageFromNCBI() to roll up your own org.Am.eg.db package, please come back with a precise description of the problem. Thanks!
>
> Cheers,
> H.
>
>>
>> Vanessa
>>
>> -----Original Message-----
>> From: Hervé Pagès [mailto:hpages at fhcrc.org]
>> Sent: Monday, February 27, 2012 2:51 PM
>> To: Corby, Vanessa
>> Cc: bioconductor at r-project.org
>> Subject: Re: [BioC] Making use of the Apis mellifera assembly 2 data
>> in goSeq
>>
>> Vanessa,
>>
>> On 02/27/2012 12:04 PM, Corby, Vanessa wrote:
>>> Page 3 of the goseq documentation states
>>>
>>> "In order to link GO categories to genes, goseq uses the organism packages from Bioconductor.
>>> These packages are named org.<Genome>.<ID>.db, where<Genome>    is a
>>> short string identifying the genome and<ID>    is a short string
>>> identifying the gene identi_er. Currently, goseq will automatically
>>> retrieve the mapping between GO categories and genes from the relevant package (as long as it is installed) for commonly used genome/ID combinations."
>>>
>>> Let's say I want to use the organism package for the Apis mellifera version 2 genome, a supported genome according to the goseq supportedGenomes() command.  I see that there are several packages that follow the naming convention org.<Genome>.<ID>.db, but none of these is for the Apis version 2 genome.  What organism package do I install for Apis mellifera 2?  Can I use BSgenome.Amellifera.UCSC.apiMel2 even though it does not follow the proper naming scheme?
>>
>> The org.<Genome>.<ID>.db packages contain annotations (more precisely mappings between gene ids and other kinds of ids). The BSgenome.* packages (like Amellifera.UCSC.apiMel2) contain no annotations, only genomes (i.e. DNA sequences). Of course there is no way you can use one to replace an org.<Genome>.<ID>.db package.
>>
>> Cheers,
>> H.
>>
>> PS: Please use the "Reply" button so emails are grouped by thread. This discussion is already splitted in 3 different threads on the list which is not going to help. Thanks!
>>
>>>
>>> Thanks.
>>>
>>> Vanessa
>>>
>>> Research Molecular Biologist
>>> USDA-ARS
>>> Carl Hayden Bee Research Center
>>> 2000 E. Allen Rd., Tucson, AZ  85719
>>>
>>> (520) 647-9269
>>>
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>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319