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Old 10-22-2014, 12:01 PM   #1
Parharn
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Default makeOrgPackageFromNCBI for S. pombe

Hi,
Does anybody know where to look up for these parameters required for the following function? No matter how much I searched on NCBI I couldn't find it! My organism is schizosaccharomyces pombe.

Code:
makeOrgPackageFromNCBI(version = "???", 
+ author = "Some One <so@someplace.org>", 
+ maintainer = "Some One <so@someplace.org>", 
+ outputDir = ".", tax_id = "????", genus = "????", species = "????")
Thanks!
Parham

Last edited by Parharn; 10-22-2014 at 01:25 PM.
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Old 10-22-2014, 03:58 PM   #2
GenoMax
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TaxID for pombe: 4896

http://www.ncbi.nlm.nih.gov/Taxonomy...hmode=1&unlock
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Old 10-23-2014, 12:17 AM   #3
Parharn
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Yes but it requires all the parameters in order to make package.
Version, author maintainer, etc.
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Old 10-23-2014, 04:11 AM   #4
GenoMax
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Take the following as an educated guess but based on the package help page it appears that the only critical thing to provide is correct taxID, the rest of the info could be left as defaults. Have you tried this?
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Old 10-23-2014, 04:46 AM   #5
Parharn
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Yes and it gives error:

Code:
> library(AnnotationForge)
> makeOrgPackageFromNCBI(tax_id="4896")
Error in .isSingleString(version) : 
  argument "version" is missing, with no default
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Old 10-23-2014, 05:01 AM   #6
GenoMax
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Try this version:

Quote:
makeOrgPackageFromNCBI(version = "0.1",
+ author = "Some One <so@someplace.org>",
+ maintainer = "Some One <so@someplace.org>",
+ outputDir = ".", tax_id = "4896", genus = "Schizosaccharomyces", species = "pombe")
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Old 10-23-2014, 05:45 AM   #7
Parharn
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Thanks, I thought that is given as example. Now it worked but still I receive an error I don't know how to resolve. Can you help in that?

Code:
> makeOrgPackageFromNCBI(version = "0.1", author = "Some One <so@someplace.org>", 
+                        maintainer = "Some One <so@someplace.org>", outputDir = ".", 
+                        tax_id = "4896", genus = "Schizosaccharomyces", species = "pombe")
Loading required package: GO.db

Getting data for gene2pubmed.gz
discarding data from other organisms
Populating gene2pubmed table:
table gene2pubmed filled
Getting data for gene2accession.gz
discarding data from other organisms
Populating gene2accession table:
table gene2accession filled
Getting data for gene2refseq.gz
discarding data from other organisms
Populating gene2refseq table:
table gene2refseq filled
Getting data for gene2unigene
discarding data from other organisms
Populating gene2unigene table:
table gene2unigene filled
Getting data for gene_info.gz
discarding data from other organisms
Populating gene_info table:
table gene_info filled
Getting data for gene2go.gz
discarding data from other organisms
Populating gene2go table:
Getting blast2GO data as a substitute for gene2go
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (RS_SQLite_exec: could not execute: column name is not unique)
In addition: Warning message:
In file.remove(dbFileName) :
  cannot remove file 'org.Spombe.eg.sqlite', reason 'Permission denied'
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Old 10-23-2014, 06:25 AM   #8
GenoMax
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I can't help with that error though it appears to be related to database. You should post that on bioconductor support list.
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Old 10-23-2014, 06:36 AM   #9
Parharn
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All right I posted it to their support site now. However if you are familiar with goseq I would like to ask you to have a look on this thread I have another place. If you have a solution to that? Thanks!
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