makeTaxonomyFasta_RDP fails to read RDPclassifier databases from Frogs

[BELKHIR]

Hi,

I tried to use makeTaxonomyFasta_RDP to convert databases for RDPClassifier maintained by Frogs team (http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/readme.txt) without success.

After debugging, it seems that the problem is linked to the fact that some taxa files contains '#' character in some fields.

This will ends with a known problem in the read.table R function which use '#" as default comment character. So to solve this issue, I had to change the db <- read.table(file=fdb, sep="", stringsAsFactors=FALSE) to db <- read.table(file=fdb, sep="", comment.char="", stringsAsFactors=FALSE)

An other solution is to use read.csv instead.

Many thanks,

Khalid,