Wei Shen shenwei356

## Makefile
# ====================
#  Project Makefile
# ====================
#  User Configuration {{{1
# ====================

# Major targets {{{2
.PHONY: figs res
figs:
# [Partially redacted]

## todo-vue-example.html
<!DOCTYPE html>
<html>
    <head>
        <meta http-equiv="content-type" content="text/html; charset=UTF-8">
        <title>Todo Vue.js Example</title>
        <link rel="stylesheet"
              type="text/css"
              href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
        <script src="https://cdn.jsdelivr.net/vue/latest/vue.js"></script>
        <style type="text/css">

## the_case_for_go.md

      
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                astaxie
                / the_case_for_go.md
            
            
              Created
              May 5, 2013 16:00
            
          
    The Case For Go


Iron.io: How We Went from 30 Servers to 2 with Go
Go at Google: Language Design in the Service of Software Engineering
Behind the Scenes: Big Data at Torbit
pool.ntp.org DNS server in Go
Juju at Canonical
Go at bitly
NSQ: realtime distributed message processing at scale


## harness.c
#define _XOPEN_SOURCE 700
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>

extern void pospopcnt_reg(int accum[8], const char *buf, size_t len);
extern void pospopcnt_mem(int accum[8], const char *buf, size_t len);

extern void

## mem.s
#include "textflag.h"

// func PospopcntMem(counts *[8]int32, buf []byte)
TEXT ·PospopcntMem(SB),NOSPLIT,$0-32
	MOVQ counts+0(FP), DI
	MOVQ buf_base+8(FP), SI		// SI = &buf[0]
	MOVQ buf_len+16(FP), CX		// CX = len(buf)

	SUBQ $32, CX			// pre-subtract 32 bit from CX
	JL scalar

## PythonTipsTricksAndIdioms.html
<p>
    My programming language of preference is python for the simple reason that I feel I write better code faster with it then I do with other languages.  However also has a lot of nice tricks and idioms to do things well.  And partly as a reminder to myself to use them, and partly because I thought this might be of general interest I have put together this collection of some of my favourite idioms.  I am also putting this on <a href="https://gist.github.com/codefisher/9d7993ddbf404c505128">gist.github.com</a> so that anyone that wants to contribute there own things can, and I will try and keep this post up to date.
</p>

<h2>enumerate</h2>

<p>
    A fairly common thing to do is loop over a list while also keeping track of what index we are up to.  Now we could use a <code>count</code> variable, but python gives us a nicer syntax for this with the <code>enumerate()</code> function.

<script src="https://gist.github.com/codefisher/9d7993ddbf404c505128.js?file=enumerate.py"></script>

## rotate_assembly.pl
#!/usr/bin/env perl
#
# rotates and (if necessary reverse complements) an assembly of a circular genome
# so that it starts with the sequence having the best blast hit to a gene database,
# e.g. dnaA
#
# depends on blastn being installed
#
# Example usage:
# rotate_assembly.pl assembly.fasta  dnaA.fa > rotated_assembly.fa

## inthash.c
/*
  For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k), which means
  hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is the inversion of
  hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x, mask), mask) == x.
*/

// Thomas Wang's integer hash functions. See <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot.
uint64_t hash_64(uint64_t key, uint64_t mask)
{
	key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;

## match.c
# gcc -Wall -o match match.c && ./match
#


#include <stdio.h>
#include <string.h>
#include <regex.h>


## gist:e051898d129b44e2f502
package main

import (
	"bufio"
	"encoding/csv"
	"encoding/json"
	"fmt"
	"io"
	"os"
	"path/filepath"
	# ====================
	# Project Makefile
	# ====================
	# User Configuration {{{1
	# ====================

	# Major targets {{{2
	.PHONY: figs res
	figs:
	# [Partially redacted]
	<!DOCTYPE html>
	<html>
	<head>
	<meta http-equiv="content-type" content="text/html; charset=UTF-8">
	<title>Todo Vue.js Example</title>
	<link rel="stylesheet"
	type="text/css"
	href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
	<script src="https://cdn.jsdelivr.net/vue/latest/vue.js"></script>
	<style type="text/css">
	#define _XOPEN_SOURCE 700
	#include <stdio.h>
	#include <stdlib.h>
	#include <string.h>
	#include <time.h>

	extern void pospopcnt_reg(int accum[8], const char *buf, size_t len);
	extern void pospopcnt_mem(int accum[8], const char *buf, size_t len);

	extern void
	#include "textflag.h"

	// func PospopcntMem(counts *[8]int32, buf []byte)
	TEXT ·PospopcntMem(SB),NOSPLIT,$0-32
	MOVQ counts+0(FP), DI
	MOVQ buf_base+8(FP), SI // SI = &buf[0]
	MOVQ buf_len+16(FP), CX // CX = len(buf)

	SUBQ $32, CX // pre-subtract 32 bit from CX
	JL scalar
	<p>
	My programming language of preference is python for the simple reason that I feel I write better code faster with it then I do with other languages. However also has a lot of nice tricks and idioms to do things well. And partly as a reminder to myself to use them, and partly because I thought this might be of general interest I have put together this collection of some of my favourite idioms. I am also putting this on <a href="https://gist.github.com/codefisher/9d7993ddbf404c505128">gist.github.com</a> so that anyone that wants to contribute there own things can, and I will try and keep this post up to date.
	</p>

	<h2>enumerate</h2>

	<p>
	A fairly common thing to do is loop over a list while also keeping track of what index we are up to. Now we could use a <code>count</code> variable, but python gives us a nicer syntax for this with the <code>enumerate()</code> function.

	<script src="https://gist.github.com/codefisher/9d7993ddbf404c505128.js?file=enumerate.py"></script>
	#!/usr/bin/env perl
	#
	# rotates and (if necessary reverse complements) an assembly of a circular genome
	# so that it starts with the sequence having the best blast hit to a gene database,
	# e.g. dnaA
	#
	# depends on blastn being installed
	#
	# Example usage:
	# rotate_assembly.pl assembly.fasta dnaA.fa > rotated_assembly.fa
	/*
	For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k), which means
	hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is the inversion of
	hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x, mask), mask) == x.
	*/

	// Thomas Wang's integer hash functions. See <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot.
	uint64_t hash_64(uint64_t key, uint64_t mask)
	{
	key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;
	# gcc -Wall -o match match.c && ./match
	#


	#include <stdio.h>
	#include <string.h>
	#include <regex.h>
	package main

	import (
	"bufio"
	"encoding/csv"
	"encoding/json"
	"fmt"
	"io"
	"os"
	"path/filepath"