Merge pull request #1 from daviortega/f-get-fasta-from-stable-id

getFasta

bin/getFastaFromStableIds-cli.js

@@ -0,0 +1,16 @@
+#!/usr/bin/env node
+'use strict'
+const shell = require('shelljs')
+const path = require('path')
+const figlet = require('figlet')
+const chalk = require('chalk')
+
+const args = process.argv.slice(2).join(' ')
+const script = path.resolve(__dirname, '../cli-scripts/getFasta.js')
+const path2bunyan = path.resolve(__dirname, '..', 'node_modules/.bin/bunyan')
+
+const splash = figlet.textSync('bitkJS-getFasta', {horizontalLayout: 'fitted'})
+console.log(chalk.cyan(splash))
+console.log(chalk.red('\t\t\t\t\t\t\t   by Davi Ortega'))
+
+shell.exec('node ' + script + ' ' + args + ' | ' + path2bunyan + ' --color')

cli-scripts/getFasta.js

@@ -0,0 +1,53 @@
+#!/usr/bin/env node
+'use strict'
+
+let path = require('path'),
+	ArgumentParser = require('argparse').ArgumentParser,
+	getFasta = require('../src/getFastaFromStableIds'),
+	fs = require('fs')
+
+let parser = new ArgumentParser({
+	addHelp: true,
+	description: 'Makes FASTA file from MiST3 stableID'
+})
+
+parser.addArgument(
+	'input',
+	{
+		help: 'Text file with stable IDs. One per line'
+	}
+)
+parser.addArgument(
+	['-o', '--output'],
+	{
+		help: 'name of the output file',
+		defaultValue: 'bitk3.fa'
+	}
+)
+
+parser.addArgument(
+	['--skipBad'],
+	{
+		help: 'Skip bad stable Ids',
+		defaultValue: false,
+		nargs: 0
+	}
+)
+
+let args = parser.parseArgs()
+
+if (args.output === 'bitk3.fa')
+	args.output = args.input.replace(/\.([a-z]|[A-Z]){2,4}$/, '.bitk3.fa')
+
+const options = (args.skipBad) ? {keepGoing: true} : {keepGoing: false}
+
+console.log(args)
+const rawData = fs.readFileSync(path.resolve(args.input)).toString()
+const stableIds = rawData.split('\n')
+
+while (stableIds.indexOf('') !== -1) {
+	const index = stableIds.indexOf('')
+	stableIds.splice(index, 1)
+}
+console.log(options)
+getFasta(stableIds, args.output, options)