library(haplotypes)
library(ape)
rm(list = ls())
dir()
#load data
seq<-read.fas("c02AOwog.fas")
#define haplotypes
hap<-haplotypes::haplotype(seq)
hap
length(hap@haplist)
#change name of haplotype from 01 to...
names(hap@haplist)
Hnum<-sprintf('%0.2d', seq(1:base::nrow(hap@sequence)))
names(hap@haplist)<-Hnum
names(hap@haplist)

#Now obtain genotype table for this marker 
hap.tab<-data.frame(lNames = rep(names(hap@haplist), lapply(hap@haplist, length)), lVal = unlist(hap@haplist))
head(hap.tab)
dim(hap.tab)

#table
hap.tab2<-hap.tab[order(hap.tab[,2]),]
head(hap.tab2)
base::as.data.frame(gsub("(2)","",seq@seqnames, fixed=T))->id
dim(id)
dim(hap.tab2)
table(id[,1],hap.tab2[,1])->tab
dim(tab)
head(tab,100)

#write table
write.table(tab,"C02_geno.txt")

#write DNA seq of haplotypes
hap@sequence->haplo
rownames(haplo)<-Hnum
write.dna(haplo, "hapC02.fas", format="fasta")