problem in df2genind when alleles encoding contain a .

[jgx65]

I stumbled on a little bug in df2genind when some alleles encoding contain a dot:

dat<-data.frame(pop=c(1,1,2,2),loc1=c("1/1","1/2","1.1/2","2/2"),loc2=c("1/1","1/2","1/2","2/2"))
(datgi<-df2genind(dat[,-1],sep="/",pop=dat[,1]))

If the dot is replaced by e.g. a dash, no problems:

dat<-data.frame(pop=c(1,1,2,2),loc1=c("1/1","1/2","1_1/2","2/2"),loc2=c("1/1","1/2","1/2","2/2"))
(datgi<-df2genind(dat[,-1],sep="/",pop=dat[,1]))

Any chance to either fix it or warn that dots should not enter allele encoding?

[zkamvar]

Which is the more desirable outcome?

• throw error and let user fix it
• throw warning and replace dot with underscore

There's currently a mechanism to do this with locus names, but not with alleles.

[EricArcher]

I vote for "throw warning and replace dot with underscore". This would work unless the underscore causes other issues, like it is already being used as a separator. In which case, maybe replacing with something ugly like a # would make the replacement obvious and unlikely to cause other conflicts...

[thierrygosselin]

I had the same issue last week and now change the dot to : to avoid potential problems with underscore.

[thibautjombart]

My vote goes to option 2: send a warning and replace with underscore

[zkamvar]

I've addressed this so that underscores are still allowable separators.

input	fix
1/1.1	1/1_1
1_1.1	1_1p1

[thibautjombart]

Cool. Pull request? ;)

[zkamvar]

Whoops. Already on master.

Sent from my iPhone

On Mar 2, 2016, at 06:07, Thibaut Jombart notifications@github.com wrote:

Cool. Pull request? ;)

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[thibautjombart]

Perfect!

Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR https://twitter.com/TeebzR

On 2 March 2016 at 15:39, Zhian N. Kamvar notifications@github.com wrote:

Whoops. Already on master.

Sent from my iPhone

On Mar 2, 2016, at 06:07, Thibaut Jombart notifications@github.com
wrote:

Cool. Pull request? ;)

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