[adegenet-forum] DNAbin and pop

[Rita Castilho]

Hi!
I am new to R and I have a lot of trouble in going from a phylip or fasta file to a genind object or fasta2DNAbin containing pop information.
My files are always phylip or fasta files, and sequences have a reference composed of an di-alpha followed by 4 numeric digits (e.g. CD1495). The first two letters determine the population to which the sequence belongs to.

Is there a quick way to do it instead of doing this, as the grouping factor can be easily deduced from the current individual labels, saving the task of read that info R separately?

#reading data
dna<- fasta2DNAbin('data.fas')
# setting pops
data.pop<- as.factor(rep(c('AD', 'CD', 'FR', 'GE', 'RE', 'OT', 'YU', 'AU'), c(17,11,12,12, 25, 14,  13,  20)))

Many thanks
Rita

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