bedapub/ribiosannotation

Annotate features (genes, mRNAs, proteins, ...) with ribios

ribiosannotation's Issues

getHumanOrthologs error

Dear David,
I am running some templates from biokitr and found out an issue with mouse <-> human orthologs. My dataset is mouse but not all of genes were being annotated with the human ortholog, despite they being well known (e.g. Cxcl11 = CXCL11). I went to the code, and it uses ribiosAnnotation function:

orths <- data.table(getHumanOrthologs(organism, useRibios = TRUE))

This function can have 2 routes if we have ribiosAnnotation credentials (which I have now in my home as specified)
However, the function fails because of the following error:

Error in rjson::fromJSON(file = file) : not all data was parsed (570 chars were parsed out of a total of 950 chars)

Have you encounter this before?
I have tested with R4.1.2 and R4.2.0 (sHPC).
Thanks, Martha

ribiosCon generates invalid connection string

Hello!
When using ribiosAnnotation::humanUniqOrtholog(ids)

In ribiosCon, I'm getting some weird string for the connection:

str <- ribiosAnnotation:::jdbcConnectString(user, password, connection$host, connection$port, connection$service_name)

str
[1] "jdbc:oracle:thin:/@:/"
con <- DBI::dbConnect(drv, str)
Error in .jcall(drv@jdrv, "Ljava/sql/Connection;", "connect", as.character(url)[1], :
java.sql.SQLRecoverableException: IO Error: Invalid connection string format, a valid format is: "//host[:port][/service_name]"

Interestingly this only happens when running ribiosAnnotation from a container.
Parameters for the jdbcConnectString() function (user, password, etc...) are all NULL in this case, but I don't know why.

it is not possible to call ribiosAnnotation::annotateXXX

because dbname, etc., are not defined if the package is not loaded

annotateGeneSymbols, annotateRefSeqs, and annotateAnyIDs are not working

And for ensembl transcripts and proteins we need new functions

gtiTaxAnnotation fails