Bruno Vieira bmpvieira

## pca.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]

## lonlat2utm.R
#!/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"

## youtubePlaylistParser.js
/*
  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');

## getMycorLinks.coffee
# 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

## getMycorSequences.coffee
# 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 (mail@bmpvieira.com)

## blastXMLtoJSON.coffee
# blastXMLtoJSON.coffee | 2013 Bruno Vieira [mail@bmpvieira.com]
#
# 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

## watable-controller.coffee
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()

## docker-osx-install.sh
#!/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.

## index.js
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")

## dnadigest-datasearch.html
<!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 -->
	#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]
	#!/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"
	/*
	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');
	# 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
	# 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 (mail@bmpvieira.com)
	# blastXMLtoJSON.coffee \| 2013 Bruno Vieira [mail@bmpvieira.com]
	#
	# 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
	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()
	#!/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.
	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")
	<!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 -->