JervenBolleman’s gists

JervenBolleman / gfaToTurtle.awk

Created August 27, 2020 17:07

	#!/usr/bin/awk -f
	BEGIN {
	print "prefix vg:<http://biohackathon.org/resource/vg> "
	print "prefix faldo:<http://biohackathon.org/resource/faldo> "
	print "prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> "
	print "prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
	print "prefix node:<"node_iri_base">"
	}
	{
	if ($1=="S"){

JervenBolleman / gist:60cc9dd13614c05fe9743519cd6ef5aa

Created December 4, 2018 11:13

Let virtuoso discover all sparql endpoints in wikidata and use it to improve federations capabilities

	for iri in $(wget -q --header "accept:text/csv" "https://query.wikidata.org/sparql?query=SELECT DISTINCT ?iri WHERE { [] wdt:P5305 ?iri }" -O -\|grep -oP '^http[\S]+')
	do
	echo "isql $port $user $password exec='LOAD SERVICE <$iri> DATA;'";
	done

JervenBolleman / spinner.svg

Created February 22, 2017 07:15

Very small SVG to create a spinning image

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JervenBolleman / gist:63d8757cddee1e1d4594b9b42c127c71

Last active February 16, 2017 15:25

Fix illegal encoded high/low surrogate pairs.

	StringBuilder f = new StringBuilder(w.length());
	for (int i = 0; i < w.length(); i++)
	{
	char c = w.charAt(i);
	if (c >= 0xD800 && c <= 0xD8FF)
	{
	int h = ((c - 0xD800) * 0x400);
	int l = ((w.charAt(++i) - 0xDC00) + 0x10000);
	f.append((char) (h + l));
	}

JervenBolleman / getServiceDescription.sh

Created September 8, 2014 11:18

Get a SPARQL 1.1 service description

wget -S "http://beta.sparql.uniprot.org/" --header "Accept:application/rdf+xml" -O - | less

JervenBolleman / GC7.java

Created August 25, 2014 12:27

GC7 GC count using binary encoded nucleotides for speed (requires converting a fasta file first)

	package gc;

	import java.io.ByteArrayOutputStream;
	import java.io.File;
	import java.io.FileInputStream;
	import java.io.FileOutputStream;
	import java.io.IOException;
	import java.io.InputStream;
	import java.io.RandomAccessFile;
	import java.nio.ByteBuffer;

JervenBolleman / gc_ds_wholefile_tbl_parallel_size.c

Created August 12, 2014 11:51

GC count in c but allocating the correc file size

	#include <stdio.h>
	#include <stdlib.h>
	#define MAXFLEN 2600000000 /* Larger than the file. */
	#include <sys/stat.h>

	int main()
	{
	char tablegc[256];
	char tableat[256];
	int gc=0;

JervenBolleman / GC6.java

Created August 12, 2014 10:44

GC6 threaded GC count using table (is faster than bit fiddling

	package gc;

	import java.io.IOException;
	import java.io.RandomAccessFile;
	import java.nio.ByteBuffer;
	import java.nio.MappedByteBuffer;
	import java.nio.channels.FileChannel;
	import java.util.ArrayList;
	import java.util.Iterator;
	import java.util.List;

JervenBolleman / GC5.java

Created August 12, 2014 07:28

GC 5 threaded GC count in java

	package gc;

	import java.io.IOException;
	import java.io.RandomAccessFile;
	import java.nio.ByteBuffer;
	import java.nio.MappedByteBuffer;
	import java.nio.channels.FileChannel;
	import java.util.ArrayList;
	import java.util.Iterator;
	import java.util.List;

JervenBolleman / GC3

Created August 11, 2014 13:45

Mapped file, same branchless gc counting

	package gc;

	import java.io.IOException;
	import java.io.RandomAccessFile;
	import java.nio.ByteBuffer;
	import java.nio.MappedByteBuffer;
	import java.nio.channels.FileChannel;


	public class GC3

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