Pau Carrió pauca

## R_chem_snippets.R

# CAS -> smiles with CACTUS server
sapply(cas, function(id){
  require(RCurl)
  return(getURL(paste("http://cactus.nci.nih.gov/chemical/structure/",id,"/smiles",sep="")))
})

## gz.scala

import java.io._
import java.util.zip._
import scala.io.Source

var in   = new GZIPInputStream(new FileInputStream("test.gz"))
// write setup in different objects to close later properly (important for big files )
var fos  = new FileOutputStream("test2.gz")
var gzos = new GZIPOutputStream( fos )
var w    = new PrintWriter(gzos)

## elapsedTime.scala
// from https://biercoff.com/easily-measuring-code-execution-time-in-scala/

def time[R](block: => R): R = {
    val t0 = System.nanoTime()
    val result = block    // call-by-name
    val t1 = System.nanoTime()
    println("Elapsed time: " + (t1 - t0) + "ns")
    result
}

## andVsAndAnd.scala


def f1 = {
    println("f1")
    true
}

def f2 = {
    println("f2")

## examplePasteAndShow.html
<!doctype html>
<html>
<head>
    <meta charset="utf-8">
    <title>Paste&Go</title>
    <script src="https://code.jquery.com/jquery-3.1.1.min.js" ></script>
    <script>

$( document ).ready(function() {
    console.log( "ready!" );

## RqcScript.R
library(Rqc)
fs <- "corrupted.fastq"
qa <- rqcQA(fs,sample=F)
sessionInfo()

## replaceSymLinks.sh
# loop over symbolik links in current directory
for f in `find . -maxdepth 1 -type l ` ; do
    # get symlink destination
    g=` readlink $f `
    # move original to directory
    cp -f $g .
    # clean
    if [ $? == 0 ]; then
        rm -f $g
        rm -f $f

## StoreRocksDB.scala
import java.io.File
import org.rocksdb._
import org.rocksdb.util.SizeUnit
import scala.collection.JavaConversions._

// build.sbt
// name := "RocksDB"
// version := "0.1"
// scalaVersion := "2.12.0"
// libraryDependencies += "org.rocksdb" % "rocksdbjni" % "5.0.1"

## AkkaStreamTemplate.scala

/*

build.sbt

name := "AkkaStreamTemplate"
version       := "0.1-SNAPSHOT"
scalaVersion  := "2.12.2"
libraryDependencies ++= {
  Seq(

## binaryDistances.R
# http://www.sequentix.de/gelquest/help/distance_measures.htm

bdist <- function( x, y , method ){
  a <- sum( x == 1 & y == 1)
  b <- sum( x == 1 & y == 0)
  c <- sum( x == 0 & y == 1)
  d <- sum( x == 0 & y == 0)

  switch(method,
         tanimoto = (a+d)/(a+2*(b+c)+d),

	# CAS -> smiles with CACTUS server
	sapply(cas, function(id){
	require(RCurl)
	return(getURL(paste("http://cactus.nci.nih.gov/chemical/structure/",id,"/smiles",sep="")))
	})

	import java.io._
	import java.util.zip._
	import scala.io.Source

	var in = new GZIPInputStream(new FileInputStream("test.gz"))
	// write setup in different objects to close later properly (important for big files )
	var fos = new FileOutputStream("test2.gz")
	var gzos = new GZIPOutputStream( fos )
	var w = new PrintWriter(gzos)
	// from https://biercoff.com/easily-measuring-code-execution-time-in-scala/

	def time[R](block: => R): R = {
	val t0 = System.nanoTime()
	val result = block // call-by-name
	val t1 = System.nanoTime()
	println("Elapsed time: " + (t1 - t0) + "ns")
	result
	}
	<!doctype html>
	<html>
	<head>
	<meta charset="utf-8">
	<title>Paste&Go</title>
	<script src="https://code.jquery.com/jquery-3.1.1.min.js" ></script>
	<script>

	$( document ).ready(function() {
	console.log( "ready!" );
	library(Rqc)
	fs <- "corrupted.fastq"
	qa <- rqcQA(fs,sample=F)
	sessionInfo()
	# loop over symbolik links in current directory
	for f in `find . -maxdepth 1 -type l ` ; do
	# get symlink destination
	g=` readlink $f `
	# move original to directory
	cp -f $g .
	# clean
	if [ $? == 0 ]; then
	rm -f $g
	rm -f $f
	import java.io.File
	import org.rocksdb._
	import org.rocksdb.util.SizeUnit
	import scala.collection.JavaConversions._

	// build.sbt
	// name := "RocksDB"
	// version := "0.1"
	// scalaVersion := "2.12.0"
	// libraryDependencies += "org.rocksdb" % "rocksdbjni" % "5.0.1"

	/*

	build.sbt

	name := "AkkaStreamTemplate"
	version := "0.1-SNAPSHOT"
	scalaVersion := "2.12.2"
	libraryDependencies ++= {
	Seq(
	# http://www.sequentix.de/gelquest/help/distance_measures.htm

	bdist <- function( x, y , method ){
	a <- sum( x == 1 & y == 1)
	b <- sum( x == 1 & y == 0)
	c <- sum( x == 0 & y == 1)
	d <- sum( x == 0 & y == 0)

	switch(method,
	tanimoto = (a+d)/(a+2*(b+c)+d),