R/Utils.R
In carltonyfakhry/InvenireSRNA: Invenire Small RNA
# This function gets the minimum free energies for a set of positive examples
getAllMinimumEnergies <- function(fastaFile){
# Init commands to call the ViennaRNA package in terminal
RNAfold = 'RNAfold -p'
# Read in the FASTA file
fasta = readBStringSet(fastaFile, use.names = T)
# For each sequence in the FASTA file, get the minimum free energy associated with the secondary structures
minimum_energies <- c()
for(i in 1:length(fasta)){
rna = as.character(fasta[[i]])
split_seq <- strsplit(rna, split = "")[[1]]
if(!all(split_seq %in% c("A","a","U","u","G","g","T","t","C","c"))){
next
}
rna = tolower(rna)
rna = gsub("t", "u", rna)
# Get the minimum free energy
structs = system(RNAfold, intern = T,wait = TRUE, input = rna)
min_energy <- as.numeric(str_match_all(structs[2],"\\(([ ]*-{0,1}[0-9]*\\.{0,1}[0-9]*)\\)$")[[1]][1,2]) # grep the minimum free energy
minimum_energies <- c(minimum_energies, min_energy)
}
return(minimum_energies)
}
# This function generates the features of the negative sequences
getNegativeSequencesFeatures <- function(fastaFile, min_energy, max_energy){
# Init commands to call the ViennaRNA package in terminal
RNAsubopt = 'RNAsubopt -p 1000'
RNAfold = 'RNAfold -p'
# Init commands to call python program altschulEriksonDinuclShuffleFasta.py to shuffle sequences
python_shuffle_file = paste(system.file(package="InvenireSRNA"), "altschulEriksonDinuclShuffleFasta.py", sep="/")
Shuffle = paste("python", python_shuffle_file, sep = " ")
# Read FASTA file
fasta = readBStringSet(fastaFile, use.names = T)
# Feature matrix
D = matrix(0, nrow = 0, ncol = 514)
# Generate a feature vector for each sequence in the fasta file
for(i in 1:length(fasta)){
# Make sure sequence is valid
rna = as.character(fasta[[i]])
split_seq <- strsplit(rna, split = "")[[1]]
if(!all(split_seq %in% c("A","a","U","u","G","g","T","t","C","c"))){
next
}
rna = tolower(rna)
rna = gsub("t", "u", rna)
# Iterate to find a minimum free energy from the ensemble of secondary structures which is in the acceptable range.
# If no suitable minimum free energy is found, then ignore the sequence, and do no generate features for it.
for(j in 1:100){
shuffled_rna = system(Shuffle, intern = T,wait = TRUE, input = rna) # shuffle sequences
struct = system(RNAfold, intern = T,wait = TRUE, input = shuffled_rna) # get minimum free energy
shuffled_rna = tolower(shuffled_rna)
shuffled_rna = gsub("t", "u", shuffled_rna)
temp_min_energy <- as.numeric(str_match_all(struct[2],"\\(([ ]*-{0,1}[0-9]*\\.{0,1}[0-9]*)\\)$")[[1]][1,2]) # grep minimum free energy
if(temp_min_energy <= max_energy & temp_min_energy >= min_energy){
structs = system(RNAsubopt, intern = T, wait = TRUE, input = shuffled_rna) # generate sample of secondary structures to generate features
new_feat = InvenireSRNA:::get_features(shuffled_rna, structs)
D = rbind(D, new_feat)
break
}
}
}
return(D)
}
# Function to generate the Boltzmann Triplet Features for sequences in a FASTA file
getBoltzmanTripletFeatures = function(fastaFile){
# Init the commands to call the ViennaRNA package in terminal
RNAsubopt = 'RNAsubopt -p 1000'
# Read in the FASTA file
fasta = readBStringSet(fastaFile, use.names = T)
# Iterate through the FASTA file and generate the feature vector for each sequence
D = matrix(0, nrow = 0, ncol = 514)
for(i in 1:length(fasta)){
# Make sure the sequence is valid
rna = as.character(fasta[[i]])
split_seq <- strsplit(rna, split = "")[[1]]
if(!all(split_seq %in% c("A","a","U","u","G","g","T","t","C","c"))){
next
}
rna = tolower(rna)
rna = gsub("t", "u", rna)
structs = system(RNAsubopt, intern = T, wait = TRUE, input = rna)
new_feat = InvenireSRNA:::get_features(rna, structs)
D = rbind(D, new_feat)
}
return(D)
}
# Get the names of features
getFeatureNames = function(){
featurenames = c("aaa000","aaa001","aaa010","aaa011","aaa100","aaa101","aaa110","aaa111","aau000","aau001",
"aau010","aau011","aau100","aau101","aau110","aau111","aac000","aac001","aac010","aac011",
"aac100","aac101","aac110","aac111","aag000","aag001","aag010","aag011","aag100","aag101",
"aag110","aag111","aua000","aua001","aua010","aua011","aua100","aua101","aua110","aua111",
"auu000","auu001","auu010","auu011","auu100","auu101","auu110","auu111","auc000","auc001",
"auc010","auc011","auc100","auc101","auc110","auc111","aug000","aug001","aug010","aug011",
"aug100","aug101","aug110","aug111","aca000","aca001","aca010","aca011","aca100","aca101",
"aca110","aca111","acu000","acu001","acu010","acu011","acu100","acu101","acu110","acu111",
"acc000","acc001","acc010","acc011","acc100","acc101","acc110","acc111","acg000","acg001",
"acg010","acg011","acg100","acg101","acg110","acg111","aga000","aga001","aga010","aga011",
"aga100","aga101","aga110","aga111","agu000","agu001","agu010","agu011","agu100","agu101",
"agu110","agu111","agc000","agc001","agc010","agc011","agc100","agc101","agc110","agc111",
"agg000","agg001","agg010","agg011","agg100","agg101","agg110","agg111","uaa000","uaa001",
"uaa010","uaa011","uaa100","uaa101","uaa110","uaa111","uau000","uau001","uau010","uau011",
"uau100","uau101","uau110","uau111","uac000","uac001","uac010","uac011","uac100","uac101",
"uac110","uac111","uag000","uag001","uag010","uag011","uag100","uag101","uag110","uag111",
"uua000","uua001","uua010","uua011","uua100","uua101","uua110","uua111","uuu000","uuu001",
"uuu010","uuu011","uuu100","uuu101","uuu110","uuu111","uuc000","uuc001","uuc010","uuc011",
"uuc100","uuc101","uuc110","uuc111","uug000","uug001","uug010","uug011","uug100","uug101",
"uug110","uug111","uca000","uca001","uca010","uca011","uca100","uca101","uca110","uca111",
"ucu000","ucu001","ucu010","ucu011","ucu100","ucu101","ucu110","ucu111","ucc000","ucc001",
"ucc010","ucc011","ucc100","ucc101","ucc110","ucc111","ucg000","ucg001","ucg010","ucg011",
"ucg100","ucg101","ucg110","ucg111","uga000","uga001","uga010","uga011","uga100","uga101",
"uga110","uga111","ugu000","ugu001","ugu010","ugu011","ugu100","ugu101","ugu110","ugu111",
"ugc000","ugc001","ugc010","ugc011","ugc100","ugc101","ugc110","ugc111","ugg000","ugg001",
"ugg010","ugg011","ugg100","ugg101","ugg110","ugg111","caa000","caa001","caa010","caa011",
"caa100","caa101","caa110","caa111","cau000","cau001","cau010","cau011","cau100","cau101",
"cau110","cau111","cac000","cac001","cac010","cac011","cac100","cac101","cac110","cac111",
"cag000","cag001","cag010","cag011","cag100","cag101","cag110","cag111","cua000","cua001",
"cua010","cua011","cua100","cua101","cua110","cua111","cuu000","cuu001","cuu010","cuu011",
"cuu100","cuu101","cuu110","cuu111","cuc000","cuc001","cuc010","cuc011","cuc100","cuc101",
"cuc110","cuc111","cug000","cug001","cug010","cug011","cug100","cug101","cug110","cug111",
"cca000","cca001","cca010","cca011","cca100","cca101","cca110","cca111","ccu000","ccu001",
"ccu010","ccu011","ccu100","ccu101","ccu110","ccu111","ccc000","ccc001","ccc010","ccc011",
"ccc100","ccc101","ccc110","ccc111","ccg000","ccg001","ccg010","ccg011","ccg100","ccg101",
"ccg110","ccg111","cga000","cga001","cga010","cga011","cga100","cga101","cga110","cga111",
"cgu000","cgu001","cgu010","cgu011","cgu100","cgu101","cgu110","cgu111","cgc000","cgc001",
"cgc010","cgc011","cgc100","cgc101","cgc110","cgc111","cgg000","cgg001","cgg010","cgg011",
"cgg100","cgg101","cgg110","cgg111","gaa000","gaa001","gaa010","gaa011","gaa100","gaa101",
"gaa110","gaa111","gau000","gau001","gau010","gau011","gau100","gau101","gau110","gau111",
"gac000","gac001","gac010","gac011","gac100","gac101","gac110","gac111","gag000","gag001",
"gag010","gag011","gag100","gag101","gag110","gag111","gua000","gua001","gua010","gua011",
"gua100","gua101","gua110","gua111","guu000","guu001","guu010","guu011","guu100","guu101",
"guu110","guu111","guc000","guc001","guc010","guc011","guc100","guc101","guc110","guc111",
"gug000","gug001","gug010","gug011","gug100","gug101","gug110","gug111","gca000","gca001",
"gca010","gca011","gca100","gca101","gca110","gca111","gcu000","gcu001","gcu010","gcu011",
"gcu100","gcu101","gcu110","gcu111","gcc000","gcc001","gcc010","gcc011","gcc100","gcc101",
"gcc110","gcc111","gcg000","gcg001","gcg010","gcg011","gcg100","gcg101","gcg110","gcg111",
"gga000","gga001","gga010","gga011","gga100","gga101","gga110","gga111","ggu000","ggu001",
"ggu010","ggu011","ggu100","ggu101","ggu110","ggu111","ggc000","ggc001","ggc010","ggc011",
"ggc100","ggc101","ggc110","ggc111","ggg000","ggg001","ggg010","ggg011","ggg100","ggg101",
"ggg110","ggg111","stem_prob", "poly_T")
return(featurenames)
}
carltonyfakhry/InvenireSRNA documentation built on May 13, 2019, 12:49 p.m.
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# This function gets the minimum free energies for a set of positive examples
getAllMinimumEnergies <- function(fastaFile){
# Init commands to call the ViennaRNA package in terminal
RNAfold = 'RNAfold -p'
# Read in the FASTA file
fasta = readBStringSet(fastaFile, use.names = T)
# For each sequence in the FASTA file, get the minimum free energy associated with the secondary structures
minimum_energies <- c()
for(i in 1:length(fasta)){
rna = as.character(fasta[[i]])
split_seq <- strsplit(rna, split = "")[[1]]
if(!all(split_seq %in% c("A","a","U","u","G","g","T","t","C","c"))){
next
}
rna = tolower(rna)
rna = gsub("t", "u", rna)
# Get the minimum free energy
structs = system(RNAfold, intern = T,wait = TRUE, input = rna)
min_energy <- as.numeric(str_match_all(structs[2],"\\(([ ]*-{0,1}[0-9]*\\.{0,1}[0-9]*)\\)$")[[1]][1,2]) # grep the minimum free energy
minimum_energies <- c(minimum_energies, min_energy)
}
return(minimum_energies)
}
# This function generates the features of the negative sequences
getNegativeSequencesFeatures <- function(fastaFile, min_energy, max_energy){
# Init commands to call the ViennaRNA package in terminal
RNAsubopt = 'RNAsubopt -p 1000'
RNAfold = 'RNAfold -p'
# Init commands to call python program altschulEriksonDinuclShuffleFasta.py to shuffle sequences
python_shuffle_file = paste(system.file(package="InvenireSRNA"), "altschulEriksonDinuclShuffleFasta.py", sep="/")
Shuffle = paste("python", python_shuffle_file, sep = " ")
# Read FASTA file
fasta = readBStringSet(fastaFile, use.names = T)
# Feature matrix
D = matrix(0, nrow = 0, ncol = 514)
# Generate a feature vector for each sequence in the fasta file
for(i in 1:length(fasta)){
# Make sure sequence is valid
rna = as.character(fasta[[i]])
split_seq <- strsplit(rna, split = "")[[1]]
if(!all(split_seq %in% c("A","a","U","u","G","g","T","t","C","c"))){
next
}
rna = tolower(rna)
rna = gsub("t", "u", rna)
# Iterate to find a minimum free energy from the ensemble of secondary structures which is in the acceptable range.
# If no suitable minimum free energy is found, then ignore the sequence, and do no generate features for it.
for(j in 1:100){
shuffled_rna = system(Shuffle, intern = T,wait = TRUE, input = rna) # shuffle sequences
struct = system(RNAfold, intern = T,wait = TRUE, input = shuffled_rna) # get minimum free energy
shuffled_rna = tolower(shuffled_rna)
shuffled_rna = gsub("t", "u", shuffled_rna)
temp_min_energy <- as.numeric(str_match_all(struct[2],"\\(([ ]*-{0,1}[0-9]*\\.{0,1}[0-9]*)\\)$")[[1]][1,2]) # grep minimum free energy
if(temp_min_energy <= max_energy & temp_min_energy >= min_energy){
structs = system(RNAsubopt, intern = T, wait = TRUE, input = shuffled_rna) # generate sample of secondary structures to generate features
new_feat = InvenireSRNA:::get_features(shuffled_rna, structs)
D = rbind(D, new_feat)
break
}
}
}
return(D)
}
# Function to generate the Boltzmann Triplet Features for sequences in a FASTA file
getBoltzmanTripletFeatures = function(fastaFile){
# Init the commands to call the ViennaRNA package in terminal
RNAsubopt = 'RNAsubopt -p 1000'
# Read in the FASTA file
fasta = readBStringSet(fastaFile, use.names = T)
# Iterate through the FASTA file and generate the feature vector for each sequence
D = matrix(0, nrow = 0, ncol = 514)
for(i in 1:length(fasta)){
# Make sure the sequence is valid
rna = as.character(fasta[[i]])
split_seq <- strsplit(rna, split = "")[[1]]
if(!all(split_seq %in% c("A","a","U","u","G","g","T","t","C","c"))){
next
}
rna = tolower(rna)
rna = gsub("t", "u", rna)
structs = system(RNAsubopt, intern = T, wait = TRUE, input = rna)
new_feat = InvenireSRNA:::get_features(rna, structs)
D = rbind(D, new_feat)
}
return(D)
}
# Get the names of features
getFeatureNames = function(){
featurenames = c("aaa000","aaa001","aaa010","aaa011","aaa100","aaa101","aaa110","aaa111","aau000","aau001",
"aau010","aau011","aau100","aau101","aau110","aau111","aac000","aac001","aac010","aac011",
"aac100","aac101","aac110","aac111","aag000","aag001","aag010","aag011","aag100","aag101",
"aag110","aag111","aua000","aua001","aua010","aua011","aua100","aua101","aua110","aua111",
"auu000","auu001","auu010","auu011","auu100","auu101","auu110","auu111","auc000","auc001",
"auc010","auc011","auc100","auc101","auc110","auc111","aug000","aug001","aug010","aug011",
"aug100","aug101","aug110","aug111","aca000","aca001","aca010","aca011","aca100","aca101",
"aca110","aca111","acu000","acu001","acu010","acu011","acu100","acu101","acu110","acu111",
"acc000","acc001","acc010","acc011","acc100","acc101","acc110","acc111","acg000","acg001",
"acg010","acg011","acg100","acg101","acg110","acg111","aga000","aga001","aga010","aga011",
"aga100","aga101","aga110","aga111","agu000","agu001","agu010","agu011","agu100","agu101",
"agu110","agu111","agc000","agc001","agc010","agc011","agc100","agc101","agc110","agc111",
"agg000","agg001","agg010","agg011","agg100","agg101","agg110","agg111","uaa000","uaa001",
"uaa010","uaa011","uaa100","uaa101","uaa110","uaa111","uau000","uau001","uau010","uau011",
"uau100","uau101","uau110","uau111","uac000","uac001","uac010","uac011","uac100","uac101",
"uac110","uac111","uag000","uag001","uag010","uag011","uag100","uag101","uag110","uag111",
"uua000","uua001","uua010","uua011","uua100","uua101","uua110","uua111","uuu000","uuu001",
"uuu010","uuu011","uuu100","uuu101","uuu110","uuu111","uuc000","uuc001","uuc010","uuc011",
"uuc100","uuc101","uuc110","uuc111","uug000","uug001","uug010","uug011","uug100","uug101",
"uug110","uug111","uca000","uca001","uca010","uca011","uca100","uca101","uca110","uca111",
"ucu000","ucu001","ucu010","ucu011","ucu100","ucu101","ucu110","ucu111","ucc000","ucc001",
"ucc010","ucc011","ucc100","ucc101","ucc110","ucc111","ucg000","ucg001","ucg010","ucg011",
"ucg100","ucg101","ucg110","ucg111","uga000","uga001","uga010","uga011","uga100","uga101",
"uga110","uga111","ugu000","ugu001","ugu010","ugu011","ugu100","ugu101","ugu110","ugu111",
"ugc000","ugc001","ugc010","ugc011","ugc100","ugc101","ugc110","ugc111","ugg000","ugg001",
"ugg010","ugg011","ugg100","ugg101","ugg110","ugg111","caa000","caa001","caa010","caa011",
"caa100","caa101","caa110","caa111","cau000","cau001","cau010","cau011","cau100","cau101",
"cau110","cau111","cac000","cac001","cac010","cac011","cac100","cac101","cac110","cac111",
"cag000","cag001","cag010","cag011","cag100","cag101","cag110","cag111","cua000","cua001",
"cua010","cua011","cua100","cua101","cua110","cua111","cuu000","cuu001","cuu010","cuu011",
"cuu100","cuu101","cuu110","cuu111","cuc000","cuc001","cuc010","cuc011","cuc100","cuc101",
"cuc110","cuc111","cug000","cug001","cug010","cug011","cug100","cug101","cug110","cug111",
"cca000","cca001","cca010","cca011","cca100","cca101","cca110","cca111","ccu000","ccu001",
"ccu010","ccu011","ccu100","ccu101","ccu110","ccu111","ccc000","ccc001","ccc010","ccc011",
"ccc100","ccc101","ccc110","ccc111","ccg000","ccg001","ccg010","ccg011","ccg100","ccg101",
"ccg110","ccg111","cga000","cga001","cga010","cga011","cga100","cga101","cga110","cga111",
"cgu000","cgu001","cgu010","cgu011","cgu100","cgu101","cgu110","cgu111","cgc000","cgc001",
"cgc010","cgc011","cgc100","cgc101","cgc110","cgc111","cgg000","cgg001","cgg010","cgg011",
"cgg100","cgg101","cgg110","cgg111","gaa000","gaa001","gaa010","gaa011","gaa100","gaa101",
"gaa110","gaa111","gau000","gau001","gau010","gau011","gau100","gau101","gau110","gau111",
"gac000","gac001","gac010","gac011","gac100","gac101","gac110","gac111","gag000","gag001",
"gag010","gag011","gag100","gag101","gag110","gag111","gua000","gua001","gua010","gua011",
"gua100","gua101","gua110","gua111","guu000","guu001","guu010","guu011","guu100","guu101",
"guu110","guu111","guc000","guc001","guc010","guc011","guc100","guc101","guc110","guc111",
"gug000","gug001","gug010","gug011","gug100","gug101","gug110","gug111","gca000","gca001",
"gca010","gca011","gca100","gca101","gca110","gca111","gcu000","gcu001","gcu010","gcu011",
"gcu100","gcu101","gcu110","gcu111","gcc000","gcc001","gcc010","gcc011","gcc100","gcc101",
"gcc110","gcc111","gcg000","gcg001","gcg010","gcg011","gcg100","gcg101","gcg110","gcg111",
"gga000","gga001","gga010","gga011","gga100","gga101","gga110","gga111","ggu000","ggu001",
"ggu010","ggu011","ggu100","ggu101","ggu110","ggu111","ggc000","ggc001","ggc010","ggc011",
"ggc100","ggc101","ggc110","ggc111","ggg000","ggg001","ggg010","ggg011","ggg100","ggg101",
"ggg110","ggg111","stem_prob", "poly_T")
return(featurenames)
}
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