matrix.js

var fs = require('fs');

function MatrixSearch(file, search) {
  var repo = fs.readFileSync(file, {
    encoding: 'utf8'
  }).trim();

  this.matrixSize = search.length
  this.matrices = this.chunk(repo.split('\n').map(function(line) {
    return this.chunk(line.split(''), this.matrixSize);
  }, this), this.matrixSize).map(function(chunk) {
    return this.matrix(chunk, this.matrixSize);
  }, this);
}

MatrixSearch.prototype.matrix = function(rows, size) {
  if (rows.length != size) {
    throw new Error('Not enough row data');
  }

  var matrix = new Array(size);

  for (var i = 0; i < matrix.length; i++) {
    var matrixRow = new Array(size);

    for (var j = 0; j < matrixRow.length; j++) {
      matrixRow[j] = rows[i][j];
    }

    matrix[i] = matrixRow;
  }

  return matrix;
};

MatrixSearch.prototype.chunk = function(arr, size) {
  var chunks = new Array(arr.length);

  for (var i = 0; i < arr.length; i++) {
    chunks[i] = arr.slice(i, i + size);

    if (chunks[i].length !== size) {
      delete chunks[i];
    }
  }

  return chunks.filter(function(chunk) {
    return chunk;
  });
};

new MatrixSearch('table.txt', '123');