Nothing
.make_kmer_dictionary<-function(k_nt,k_aa,gap_size_nt=c(0,1,2,3,4,5,6,7,8,9,10),gap_size_aa=c(0,1,2,3)){
#makes a dictionary for kmer combo counts depending on kmer sizes used in analysis
#only needs to be run once.
#cat('Preparing nt dictionary ...\n')
#first do nucleotidedictionary
#set k to make dictionary
#for each length in k_nt make a dictionary
k_prep_nt<-k_nt#c(1,2,3,4)
dictionaries_nt<-list()
for(i in 1:length(k_prep_nt)){
k_length<-k_prep_nt[[i]]
#set alphabet (nt)
dictionary<-c("A","C","G","T")
#find all possible kmers of current length
combn_it<-k_length
all_combs<-dictionary
while(combn_it>1){
combn_dict<-merge(dictionary,all_combs)
all_combs<-apply(combn_dict, 1, paste, collapse="")
combn_it<-combn_it-1
}#
#merge into pairs
all_pairs_of_combs<-apply(merge(all_combs,all_combs),1,paste,collapse=",")
#set counts to zero
nt_pair_dict_gen<-rep(0,length(all_pairs_of_combs))
names(nt_pair_dict_gen)<-all_pairs_of_combs#
dictionaries_nt[[i]]<-nt_pair_dict_gen
}
#give dictionaries created names that make them identifiable
names(dictionaries_nt)<-as.character(k_nt) #c("1","2","3","4")
#cat('nt dictionary Done \n')
#cat('Preparing aa dictionary ...\n')
#do the same for amino acids
k_prep_aa<-k_aa #c(1,2)
dictionaries_aa<-list()
for(i in 1:length(k_prep_aa)){
k_length<-k_prep_aa[[i]]
dictionary<-c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y","*")
combn_it<-k_length
all_combs<-dictionary
while(combn_it>1){
combn_dict<-merge(dictionary,all_combs)
all_combs<-apply(combn_dict, 1, paste, collapse="")
combn_it<-combn_it-1
}#
all_pairs_of_combs<-apply(merge(all_combs,all_combs),1,paste,collapse=",")
aa_pair_dict_gen<-rep(0,length(all_pairs_of_combs))
names(aa_pair_dict_gen)<-all_pairs_of_combs#
dictionaries_aa[[i]]<-aa_pair_dict_gen
}
names(dictionaries_aa)<-as.character(k_aa)
#create output file: 1 nt dictionary(ies) 2.aa, 3/4 record gap sizes of dictionary for nt and amino acid
dictionary_counts<-list()
dictionary_counts[[1]]<-dictionaries_nt
dictionary_counts[[2]]<-dictionaries_aa
dictionary_counts[[3]] <- gap_size_nt
dictionary_counts[[4]] <- gap_size_aa
names(dictionary_counts)<-c("nt","AA","gap_nt","gap_aa")
#cat(' Done \n')
return(dictionary_counts)
}
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