philippbayer

#!/usr/bin/python3

# This Script parses a couple of genotyping-files downloaded from openSNP.
# It supports deCODEme, FamilyTreeDNA and 23andme-files.
# If you don't like the Object Oriented Magic just comment out the lines with allSnps.append 
# and do your own magic.

# Example-Useage is name of the script followed by as many filenames as you like.
# ./megaparser.py 200.23andme.12 92.decodeme.1 [...]
# or:

philippbayer

$ python2.7 parse.py
0.797344923019

$ julia parse.jl
16789.66212272644

o.O
Tested against a 91mb big tab-delimited input-file.

With a 800mb big file:

philippbayer

min = 1000000000
5.times do
    t = Time.now
    File.open("./backParsedTapidorContigs.csv").each do |r|
        r.split("\t")
    end
    finish = (Time.now - t)
    if finish < min
        min = finish
    end

philippbayer

-------------------------------------------------------
C++:

#include <iostream>
#include <string>
#include <fstream>
#include <boost/tokenizer.hpp>
#include <vector>
#include <iterator>
#include <sys/time.h>

philippbayer

return_dict = {}
for line in file_handle:
	line_list = line.split()
	if line_list[0] in return_dict.keys():
		return_dict[line_list[0]].append(line_list)
	else:
		return_dict[line_list[0]] = [line_list]

philippbayer

return_dict = {}
for line in file_handle:
	line_list = line.split()
	try:
	        return_dict[line_list[0]].append(line_list)
	except KeyError:
		return_dict[line_list[0]] = [line_list]

philippbayer

from collections import defaultdict
d = defaultdict(list)
for line in file_handle:
    line_list = line.split
    d[line_list[0]].append(line_list)

philippbayer

package main

import (
	"bufio"
	"fmt"
	"os"
)

func main() {
	f, err := os.Open("./example")

philippbayer

>>python -m timeit "100 + 0.0"
10000000 loops, best of 3: 0.0217 usec per loop

>>python -m timeit "float(100)"
10000000 loops, best of 3: 0.17 usec per loop

philippbayer

PRIMUS_VERBOSE=2 primusrun ./Buddha.bin.x86 
[S_API FAIL] SteamAPI_Init() failed; SteamAPI_IsSteamRunning() failed.
[S_API FAIL] SteamAPI_Init() failed; unable to locate a running instance of Steam, or a local steamclient.dll.
primus: profiling: display: 45.6 fps, 24.3% wait, 20.0% upload, 55.7% draw+swap
primus: profiling: readback: 45.9 fps, 28.0% app, 18.6% map, 53.4% wait
primus: profiling: display: 59.9 fps, 0.7% wait, 27.1% upload, 72.2% draw+swap
primus: profiling: readback: 59.8 fps, 5.1% app, 20.8% map, 74.1% wait
primus: profiling: display: 51.3 fps, 15.4% wait, 23.5% upload, 61.1% draw+swap
primus: profiling: readback: 51.3 fps, 16.6% app, 19.2% map, 64.2% wait
primus: profiling: display: 59.9 fps, 0.7% wait, 26.8% upload, 72.5% draw+swap