I couldn’t find a quick function that validates a single DNA FASTA file in javascript, so here a setup (it uses the same structure as this protein FASTA validator from the Oxford Protein Informatics Group).
function validateDNA (seq) {
//Based on: http://www.blopig.com/blog/2013/03/a-javascript-function-to-validate-fasta-sequences/
// immediately remove trailing spaces
seq = seq.trim();
// split on newlines...
var lines = seq.split('\n');
// check for header
if (seq[0] == '>') {
// remove one line, starting at the first position
lines.splice(0, 1);
}
// join the array back into a single string without newlines and
// trailing or leading spaces
seq = lines.join('').trim();
//Search for charaters that are not G, A, T or C.
if (seq.search(/[^gatc\s]/i) != -1) {
//The seq string contains non-DNA characters
return false;
/// The next line can be used to return a cleaned version of the DNA
/// return seq.replace(/[^gatcGATC]/g, "");
}
else
{
//The seq string contains only GATC
return true;
}
}
Have fun