param_base <- c("A", "C", "G", "T", "N")#o͂w
library(Biostrings)                    #pbP[W̓ǂݍ

################
###  Step 1
################
in_f <- "out_contig.fa"                #̓t@Cw肵in_fɊi[
out_f <- "result_step1.txt"            #o̓t@Cw肵out_fɊi[

fasta <- readDNAStringSet(in_f, format="fasta")#in_fŎw肵t@C̓ǂݍ
hoge <- alphabetFrequency(fasta)       #A,C,G,T,..̐ez񂲂ƂɃJEgʂhogeɊi[
obj <- is.element(colnames(hoge), param_base)#𖞂ǂ𔻒肵ʂobjɊi[
out <- apply(as.matrix(hoge[, obj]), 2, sum)#񂲂Ƃ̑aoutɊi[
write.table(out, out_f, sep="\t", append=F, quote=F, row.names=T, col.names=F)#out̒gw肵t@Cŕۑ

################
###  Step 2
################
in_f <- "out_scaffold.fa"              #̓t@Cw肵in_fɊi[
out_f <- "result_step2.txt"            #o̓t@Cw肵out_fɊi[

fasta <- readDNAStringSet(in_f, format="fasta")#in_fŎw肵t@C̓ǂݍ
hoge <- alphabetFrequency(fasta)       #A,C,G,T,..̐ez񂲂ƂɃJEgʂhogeɊi[
obj <- is.element(colnames(hoge), param_base)#𖞂ǂ𔻒肵ʂobjɊi[
out <- apply(as.matrix(hoge[, obj]), 2, sum)#񂲂Ƃ̑aoutɊi[
write.table(out, out_f, sep="\t", append=F, quote=F, row.names=T, col.names=F)#out̒gw肵t@Cŕۑ

################
###  Step 3
################
in_f <- "out_gapClosed.fa"             #̓t@Cw肵in_fɊi[
out_f <- "result_step3.txt"            #o̓t@Cw肵out_fɊi[

fasta <- readDNAStringSet(in_f, format="fasta")#in_fŎw肵t@C̓ǂݍ
hoge <- alphabetFrequency(fasta)       #A,C,G,T,..̐ez񂲂ƂɃJEgʂhogeɊi[
obj <- is.element(colnames(hoge), param_base)#𖞂ǂ𔻒肵ʂobjɊi[
out <- apply(as.matrix(hoge[, obj]), 2, sum)#񂲂Ƃ̑aoutɊi[
write.table(out, out_f, sep="\t", append=F, quote=F, row.names=T, col.names=F)#out̒gw肵t@Cŕۑ
