blastjs - npm Package Compare versions

Comparing version 1.1.0 to 1.2.0

lib/blast.js

		var fs = require('fs');
		var parseString = require('xml2js').parseString;

		var blast = {};
		var blast = {
		stringOutput: false
		};

		blast.outputString = function (bool) {
		this.stringOutput = !!(!bool \|\| bool == true);
		};

		blast.blastN = function (db, query, cb) {
		@@ -43,13 +50,6 @@ blaster('blastn', db, query, cb);
		fs.readFile(outFile, 'utf8', function (err, data) {
		if (err) {
		console.log('error reading blast output', err);
		return cb(err, null);
		} else {
		console.log(data);
		parseString(data, function (err, result) {
		return cb(err, result);
		});


		var strippedData = data.substring(data.indexOf('Length'));

		return cb(null, strippedData);
		}
		});
		@@ -66,4 +66,8 @@ }
		var outFile = outPath + generateGuid() + '.out';
		var blastCommand = type + ' -query ' + path + ' -out ' + outFile + ' -db ' + db;// + ' -outfmt 5';
		var blastCommand = type + ' -query ' + path + ' -out ' + outFile + ' -db ' + db;

		if (!this.stringOutput) {
		blastCommand += ' -outfmt 5';
		}

		run(blastCommand, function (err, stdOut, stdError) {
		@@ -70,0 +74,0 @@ postBlast(err, stdOut, stdError, outFile, cb);

package.json

		{
		"name": "blastjs",
		"version": "1.1.0",
		"version": "1.2.0",
		"description": "a blast+ wrapper",
		@@ -8,3 +8,3 @@ "homepage": "https://github.com/wookoouk/blastjs",
		"scripts": {
		"test": "mocha"
		"test": "./node_modules/mocha/bin/mocha"
		},
		@@ -26,3 +26,6 @@ "repository": {
		"xml2js": "^0.4.12"
		},
		"devDependencies": {
		"mocha": "^2.3.1"
		}
		}

README.md

		@@ -41,2 +41,4 @@ # blast.js

		blast.outputString(true); optional

		var dbPath = './example';
		@@ -43,0 +45,0 @@ var query = 'CTAATACCGAATAAGGTCAGTTAATTTGTTAATTGATGAAAGGAAGCCTT';

test/test.js

		var assert = require("assert");

		var path = require('path');

		describe('blast', function () {
		describe('#blastN', function () {
		var blast = require('../index.js');
		var dbPath = './example';
		var dbPath = path.join(__dirname + '/example');
		var query = 'CTAATACCGAATAAGGTCAGTTAATTTGTTAATTGATGAAAGGAAGCCTT';

		it('should not get an error', function () {
		it('should not get an error', function (done) {
		blast.blastN(dbPath, query, function (err, output) {
		assert.equel(null, err);
		assert.equal(err, null);
		done();
		});
		@@ -13,0 +16,0 @@ });

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