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parseFile.js
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parseFile.js
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const effictive_codons = require("./effective_condons");
get_protein_sequence = (gene_seq) => {
let protein_seq = "";
gene_seq = gene_seq.replace(/\r?\n|\r/g,"");
let gene_arr = gene_seq.match(/.{1,3}/g);
let flag = 0;
let i=0;
for (const gene of gene_arr) {
if (gene[0] == 'U') {
if (gene[1] == 'U') {
if (gene[2] == 'U' || gene[2] == 'C') {
protein_seq = protein_seq + "F";
} else if (gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "L";
}
} else if (gene[1] == 'C') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "S";
}
} else if (gene[1] == 'A') {
if (gene[2] == 'U' || gene[2] == 'C') {
protein_seq = protein_seq + "Y";
} else if (gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "STOP";
}
} else if (gene[1] == 'G') {
if (gene[2] == 'U' || gene[2] == 'C') {
protein_seq = protein_seq + "C";
} else if (gene[2] == 'A') {
protein_seq = protein_seq + "STOP";
} else if (gene[2] == 'G') {
protein_seq = protein_seq + "W";
}
}
} else if (gene[0] == 'C') {
if (gene[1] == 'U') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "L";
}
} else if (gene[1] == 'C') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "P";
}
} else if (gene[1] == 'A') {
if (gene[2] == 'U' || gene[2] == 'C') {
protein_seq = protein_seq + "H";
} else if (gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "Q";
}
} else if (gene[1] == 'G') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "R";
}
}
} else if (gene[0] == 'A') {
if (gene[1] == 'U') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[3] == 'A') {
protein_seq = protein_seq + "I";
} else if (gene[2] == 'G') {
protein_seq = protein_seq + "M";
}
} else if (gene[1] == 'C') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "T";
}
} else if (gene[1] == 'A') {
if (gene[2] == 'U' || gene[2] == 'C') {
protein_seq = protein_seq + "N";
} else if (gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "K";
}
} else if (gene[1] == 'G') {
if (gene[2] == 'U' || gene[2] == 'C') {
protein_seq = protein_seq + "S";
} else if (gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "R";
}
}
} else if (gene[0] == 'G') {
if (gene[1] == 'U') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "V";
}
} else if (gene[1] == 'C') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "A";
}
} else if (gene[1] == 'A') {
if (gene[2] == 'U' || gene[2] == 'C') {
protein_seq = protein_seq + "D";
} else if (gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "E";
}
} else if (gene[1] == 'G') {
if (gene[2] == 'U' || gene[2] == 'C' || gene[2] == 'A' || gene[2] == 'G') {
protein_seq = protein_seq + "G";
}
}
}
}
return protein_seq;
}
handleFileChosen = contents => {
let details = [];
contents = contents.split(">");
console.log(contents.length);
if (contents.length > 1) {
for (let i = 1; i < contents.length; i++) {
if (contents[i].includes("genome")) {
split_term = "genome";
} else if (contents[i].includes("Reverse")) {
split_term = "Reverse";
} else if (contents[i].includes("Forward")) {
split_term = "Forward";
} else {
console.log("Not a fasta file");
}
let content = contents[i].split(split_term);
let gene = content[1].replace(/T/g, "U");
gene = gene.replace(/\r?\n|\r/g,"");
let gene_arr = gene.match(/.{1,3}/g);
let correct = true
for (let i=0; i< gene_arr.length - 1;i++){
if(gene_arr[i].includes("UGA") || gene_arr[i].includes("UAA") || gene_arr[i].includes("UAG")){
correct = false;
}
}
if (content[1].match("[^ATGC]*")[0].length > 3) {
console.log(content[1].match("[^ATGC]*")[0])
console.log("Error in gene");
return null;
} else {
content[1] = content[1].replace(/\r?\n|\r/g, '');
let no_of_effective_codons = effictive_codons.effective_no_of_codons(content[1]);
len = content[1].length;
countA = (content[1].match(/A/g) || []).length;
countT = (content[1].match(/T/g) || []).length;
countG = (content[1].match(/G/g) || []).length;
countC = (content[1].match(/C/g) || []).length;
let protein_seq = get_protein_sequence(gene);
per = (countG + countC) * 100.0 / len;
loc = (content[0].substring(content[0].indexOf(":") + 1)).split(" ")[0];
if (loc[0] == 'c') {
let temp = loc.split("-");
loc = temp[1] + "-" + temp[0].slice(1);
}
if (loc.indexOf(",") == -1) {
details.push({
meta: content[0],
Location: loc,
Nc: no_of_effective_codons,
gene: content[1],
protein_seq: protein_seq,
count_A: countA,
count_T: countT,
count_G: countG,
count_C: countC,
length: len,
percentage_G_C: per,
correct : correct
});
}
}
}
} else {
console.log("It is not a fasta file");
}
// console.log(details[1]);
return details;
};
getDetails = data => {
let gene_details = [];
var lines = data.split(/\n/);
for (let i = 3; i < lines.length; i++) {
let x = lines[i].split(/\t/);
gene_details.push({
Location: x[0].replace("..", "-"),
Strand: x[1],
Length: x[2],
PID: x[3],
Gene: x[4],
Synonym: x[5],
Code: x[6],
COG: x[7],
Product: x[8]
});
}
return gene_details;
};
module.exports = {
handleFileChosen,
getDetails
};