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Hyungyong Kim yong27

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yong27 / broken_fastq.py
Created May 4, 2013
Extract valid data from broken fastq file.
View broken_fastq.py
def is_valid_fastq(lines):
start = lines[0].startswith('@')
middle = lines[2].startswith('+')
length = len(lines[1]) == len(lines[3])
return all([start, middle, length])
def FastqIterator(file):
lines = [file.next(), file.next(), file.next()]
for line in file:
lines.append(line)
@yong27
yong27 / hangul_python.py
Last active Dec 17, 2015
Idioms for Hangul Python programming. It's for Python 3.
View hangul_python.py
import unittest
class 유형:
def __init__(자기, *인수, **키워드인수):
자기.생성될때(*인수, **키워드인수)
class 시험사례(unittest.TestCase):
같아야함 = unittest.TestCase.assertEquals
class 배열(list):
View clock_angle.py
import unittest
from math import pi, degrees
def get_hour_angle(hour, minute=0):
angle = (hour / 6.) * pi
minute_angle = get_minute_angle(minute) / 12
return angle + minute_angle
def get_minute_angle(minute):
angle = (minute / 30.) * pi
@yong27
yong27 / clock_angle_chart.ipynb
Created May 24, 2013
Clock angle chart ipython notebook
View clock_angle_chart.ipynb
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@yong27
yong27 / geo_downloader.py
Last active May 19, 2020
GEO file downloader from query search result CSV
View geo_downloader.py
# -*- coding:utf-8 -*-
"""
GEO file downloader
Requirements
* beautifulsoup4 (pip install lxml beautifulsoup4)
* wget
Usage
1. get CSV file in the GEO browse page.
@yong27
yong27 / apply_df_by_multiprocessing.py
Last active Mar 17, 2022
pandas DataFrame apply multiprocessing
View apply_df_by_multiprocessing.py
import multiprocessing
import pandas as pd
import numpy as np
def _apply_df(args):
df, func, kwargs = args
return df.apply(func, **kwargs)
def apply_by_multiprocessing(df, func, **kwargs):
workers = kwargs.pop('workers')
View gist:1663c74272b7e685fdc2
{
"metadata": {
"name": "",
"signature": "sha256:9299994bc33725ce2fb54720efc2a7b1a7fb1e955d3914b9e8ba9de6a50bd456"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
@yong27
yong27 / metagenome_profiler.py
Created Mar 13, 2015
Metagenome basic profiler
View metagenome_profiler.py
import pandas as pd
from subprocess import Popen, PIPE
def len_fasta(filename):
p1 = Popen(['cat', filename], stdout=PIPE, stderr=PIPE)
p2 = Popen(['grep', '>'], stdin=p1.stdout, stdout=PIPE, stderr=PIPE)
p3 = Popen(['wc', '-l'], stdin=p2.stdout, stdout=PIPE, stderr=PIPE)
result, err = p3.communicate()
if p3.returncode != 0:
View Korean-social-newtork-status.json
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"[대한민국 SNS 이용현황](http://m.blog.naver.com/mobidays01/220331132165) 블로그 글에 표시된 그림을 좀 다르게 그려보자\n",
"\n",
"![](http://mblogthumb1.phinf.naver.net/20150414_20/mobidays01_14290006372183j5KB_JPEG/mobidays_sns%C0%CC%BF%EB%C7%F6%C8%B2.jpg?type=w2)"
]
@yong27
yong27 / go_term_stat.py
Created May 13, 2015
It's for counting biological_process terms which have is_a and part_of.
View go_term_stat.py
"""
It's for counting biological_process terms which have is_a and part_of.
Usage:
$ wget http://purl.obolibrary.org/obo/go.obo
$ python3 go_term_stat.py < go.obo
Main data structure