bmpvieira’s gists

bmpvieira / pca.R

Created April 10, 2012 20:05

Short PCA example with FactoMineR and ggplot2 in R

	#Copyright (c) 2012 Bruno Vieira [http://bmpvieira.com]
	#License: CC BY
	#Short PCA example with FactoMineR and ggplot2 in R

	library(FactoMineR)
	library(ggplot2)
	data = read.table("data.tsv", head=T, row.names=1)
	pca = PCA(data[,2:ncol(data)], scale.unit=T, graph=F)
	PC1 = pca$ind$coord[,1]
	PC2 = pca$ind$coord[,2]

bmpvieira / lonlat2utm.R

Created August 16, 2012 23:46

Simple R script to convert Long/Lat to UTM format

	#!/usr/bin/Rscript
	#
	#Copyright (c) 2012 Bruno Vieira [http://bmpvieira.com]
	#License: MIT
	#Description: Simple R script to convert Long/Lat to UTM format

	require("PBSmapping") \|\| install.packages("PBSmapping", dependencies=TRUE) && require("PBSmapping")
	input <- commandArgs(TRUE)[1]
	coord <- read.csv(input, header = TRUE)
	attr(coord, "projection") <- "LL"

bmpvieira / youtubePlaylistParser.js

Created October 2, 2012 16:49

Simple Youtube playlist parser using JSONStream

	/*
	author: bmpvieira
	license: WTFPL
	description: Simple Youtube playlist parser using https://github.com/dominictarr/JSONStream
	usage example: node youtubePlaylistParser.js PLt4dwg5cC5TSqHR44YK0UQ_8TSG8YtZtI \| cclive -f best -c
	*/

	var request = require('request');
	var JSONStream = require('JSONStream');

bmpvieira / getMycorLinks.coffee

Last active December 12, 2015 00:18

This script fetches all the sequences links from a MycorWeb Blast result.

	# getMycorLinks.coffee
	# This script fetches all the sequences links from a MycorWeb Blast result.
	#
	# sequences can be fetched from these links with getMycorSequences.coffee:
	# https://gist.github.com/4683075
	# results can be splitted into multiple files to run multiple instances of
	# getMycorSequences.coffee
	#
	# Dependencies: casperjs
	# Usage: casperjs getMycorLinks.coffee numberOutputFiles URL

bmpvieira / getMycorSequences.coffee

Last active December 12, 2015 00:18

This script fetches sequences from MycorWeb Blast result links.

	# getMycorSequences.coffee
	# This script fetches sequences from MycorWeb Blast result links.
	#
	# links file must be provided and can be obtained with getMycorLinks.coffee:
	# https://gist.github.com/4683065
	#
	# Dependencies: casperjs
	# Usage: casperjs getMycorSequences.coffee fileWithLinks
	# Example: casperjs getMycorSequences.coffee sequencesLinks:0-4275.txt
	# Author: Bruno Vieira ([email protected])

bmpvieira / blastXMLtoJSON.coffee

Created February 13, 2013 09:25

Convert NCBI's Blast XML results to JSON

	# blastXMLtoJSON.coffee \| 2013 Bruno Vieira [[email protected]]
	#
	# This script converts NCBI's Blast XML results to JSON
	#
	# For small files, it parses everything into a object in memory and
	# writes the result to the output file in the end.
	# For big files, it will write each Blast “Iteration” object separately,
	# one per line, to avoid memory limits.
	#
	# Usage: coffee blastXMLtoJSON.coffee blast_results.xml output.json

bmpvieira / watable-controller.coffee

Last active December 20, 2015 03:09

CoffeeScript and JavaScript examples of using WATable with Express.js and Jade, with button to download CSV.

	app.get '/watable', (req, res, next) ->
	res.render 'watable'

	app.get '/data.json', (req, res, next) ->
	UserModel.find {}, 'email firstname lastname', (err, users) ->
	return next err if err

	rows = []
	for user in users
	user = user.toObject()

bmpvieira / docker-osx-install.sh

Created January 26, 2014 20:05

Docker running natively in OSX connected to daemon running inside Vagrant

	#!/bin/bash
	# Docker running natively in OSX connected to daemon running inside Vagrant
	#
	# This allows to use Docker natively in an OSX terminal, connected to a docker
	# daemon running inside a CoreOS VM in Vagrant. Shared folder enabled through NFS.
	#
	# I tried to use [dvm](https://github.com/fnichol/dvm) but got issues with
	# networking (#4) and shared folder (#7), so I just switched to CoreOS and
	# added the settings for it to work like dvm.

bmpvieira / index.js

Created March 19, 2014 12:24 — forked from max-mapper/index.js

requirebin sketch

	var shell = require("gl-now")({clearColor: [0,0,0,0]})
	var camera = require("game-shell-orbit-camera")(shell)
	var createTileMap = require("gl-tile-map")
	var ndarray = require("ndarray")
	var terrain = require("isabella-texture-pack")
	var createAOShader = require("ao-shader")
	var glm = require("gl-matrix")
	var createShader = require("gl-shader")
	var createBuffer = require("gl-buffer")
	var createVAO = require("gl-vao")

bmpvieira / dnadigest-datasearch.html

Last active August 29, 2015 13:58

Mockup of an ideal UI/UX for searching data sets. Developed during the DNAdigest Hackday in London (5 April 2014) by @bmpvieira, @yannaspot and @owenlancaster

	<!DOCTYPE html>

	<html lang="en">
	<head>
	<meta charset="utf-8">
	<meta content="IE=edge" http-equiv="X-UA-Compatible">
	<meta content="width=device-width, initial-scale=1" name="viewport">

	<title>DNAdigest</title>
	<!-- Bootstrap -->

Bruno Vieira bmpvieira