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Focusing on hobby

Taeyoon Kim partrita

๐ŸŽฏ
Focusing on hobby
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@partrita
partrita / download.sh
Last active June 22, 2025 05:07
how to use `wget` command for NCBI GSE database.
#!/bin/bash
# ์ด ์Šคํฌ๋ฆฝํŠธ๋Š” NCBI Gene Expression Omnibus (GEO)์—์„œ GSE ์ฝ”๋“œ๋ฅผ ์‚ฌ์šฉํ•˜์—ฌ ๋ฐ์ดํ„ฐ๋ฅผ ๋‹ค์šด๋กœ๋“œํ•ฉ๋‹ˆ๋‹ค.
# 1. GSE ์ฝ”๋“œ ๋ณ€์ˆ˜ ์ •์˜
# ๋‹ค์šด๋กœ๋“œํ•˜๊ณ ์ž ํ•˜๋Š” GSE ์ฝ”๋“œ๋ฅผ ์—ฌ๊ธฐ์— ํ• ๋‹นํ•˜์„ธ์š”.
# ์˜ˆ์‹œ: GSE132555 ๋˜๋Š” ๋‹ค๋ฅธ ์œ ํšจํ•œ GSE ์ฝ”๋“œ
GSE_CODE="GSE132555"
# 2. wget ๋ช…๋ น์–ด๋ฅผ ์‚ฌ์šฉํ•˜์—ฌ ๋ฐ์ดํ„ฐ ๋‹ค์šด๋กœ๋“œ
@partrita
partrita / ladder_game.py
Last active April 18, 2024 03:04
ladder_game_generator
import random
# Define the probability
probability = 0.33
ladder_h = "โ•ฌ"
ladder_w = "โ•"
empty = "โ–‘"
def create_ladder(num_people, num_lines):
# Initialize the ladder with vertical lines
@partrita
partrita / clinicaltrial.py
Last active June 22, 2025 05:06
This Python script provides the functionality to easily retrieve clinical data and save it as a CSV file.
from pytrials.client import ClinicalTrials
import pandas as pd
import datetime as dt
import logging
# Configure logging for better feedback
logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
def get_clinical_trials_data(condition: str) -> None:
"""
@partrita
partrita / Dockerfile
Last active June 22, 2025 05:06
micromamba docker file
# ๋ฒ ์ด์Šค ์ด๋ฏธ์ง€ ์ •์˜: mambaorg/micromamba ์ด๋ฏธ์ง€์˜ ํŠน์ • ๋ฒ„์ „(1.5.1)์„ ์‚ฌ์šฉํ•ฉ๋‹ˆ๋‹ค.
# ์ด ์ด๋ฏธ์ง€๋Š” Micromamba๊ฐ€ ๋ฏธ๋ฆฌ ์„ค์น˜๋˜์–ด ์žˆ์–ด ํ™˜๊ฒฝ ์„ค์ •์„ ๋น ๋ฅด๊ณ  ์‰ฝ๊ฒŒ ํ•  ์ˆ˜ ์žˆ๋„๋ก ๋•์Šต๋‹ˆ๋‹ค.
FROM mambaorg/micromamba:1.5.1
# ํ™˜๊ฒฝ ํŒŒ์ผ ๋ณต์‚ฌ: 'environments.yml' ํŒŒ์ผ์„ Docker ์ด๋ฏธ์ง€ ๋‚ด๋ถ€์˜ '/tmp/' ๋””๋ ‰ํ† ๋ฆฌ๋กœ ๋ณต์‚ฌํ•ฉ๋‹ˆ๋‹ค.
# --chown ํ”Œ๋ž˜๊ทธ๋Š” ๋ณต์‚ฌ๋œ ํŒŒ์ผ์˜ ์†Œ์œ ์ž๋ฅผ Micromamba ์‚ฌ์šฉ์ž($MAMBA_USER)๋กœ ์„ค์ •ํ•˜์—ฌ ๊ถŒํ•œ ๋ฌธ์ œ๋ฅผ ๋ฐฉ์ง€ํ•ฉ๋‹ˆ๋‹ค.
# ์ด YAML ํŒŒ์ผ์€ ์„ค์น˜ํ•  ํŒจํ‚ค์ง€ ๋ฐ Conda ํ™˜๊ฒฝ์˜ ์ข…์†์„ฑ์„ ์ •์˜ํ•ฉ๋‹ˆ๋‹ค.
COPY --chown=$MAMBA_USER:$MAMBA_USER environments.yml /tmp/env.yml
# Conda ํ™˜๊ฒฝ ์ž๋™ ํ™œ์„ฑํ™” ์„ค์ •:

์œˆ๋„์šฐ์—์„œ Altํ‚ค <-> Ctrl ์œ„์น˜ ๋ณ€๊ฒฝ, Capslockํ‚ค๋ฅผ ํ•œ์˜ํ‚ค๋กœ

๋งฅ๊ณผ ์œˆ๋„์šฐ๋ฅผ ๋ฒˆ๊ฐˆ์•„ ์“ฐ๋‹ค๋ณด๋‹ˆ ๋งฅ์˜ ํ‚ค๋ณด๋“œ ๋ ˆ์ด์•„์›ƒ์ด ๋” ์ธ์ฒด๊ณตํ•™์ ์œผ๋กœ ๋А๊ปด์กŒ๋‹ค.

๋ฐฉ๋ฒ•

  1. ๋ฉ”๋ชจ์žฅ์„ ์—ด์–ด์„œ ์•„๋ž˜ ๋‚ด์šฉ์„ ์ €์žฅํ•œ ํŒŒ์ผ์„ ๊ฐ๊ฐ ๋งŒ๋“ ๋‹ค.
  2. key_swap.reg ํŒŒ์ผ์„ ์‹คํ–‰ํ•˜๊ณ  ์žฌ๋ถ€ํŒ…ํ•œ๋‹ค.
  3. ์›๋ž˜๋Œ€๋กœ ๋ณ€๊ฒฝ์„ ์›ํ•  ๋•Œ๋Š” reset_swap.reg์„ ์‹คํ–‰ํ•˜๊ณ  ์žฌ๋ถ€ํŒ…ํ•œ๋‹ค.
@partrita
partrita / mutant_sequence_gen.py
Created February 19, 2024 05:47
์ด ์ฝ”๋“œ๋Š” ์ฃผ์–ด์ง„ WT ๋‹จ๋ฐฑ์งˆ ์„œ์—ด์„ ๊ธฐ๋ฐ˜์œผ๋กœ ๋ฎคํ„ดํŠธ ์„œ์—ด์„ ์ƒ์„ฑํ•˜๊ณ , ์ด๋ฅผ FASTA ํ˜•์‹์œผ๋กœ ๋ณ€ํ™˜ํ•˜์—ฌ ์ถœ๋ ฅํ•˜๋Š” ์ž‘์—…์„ ์ˆ˜ํ–‰ํ•ฉ๋‹ˆ๋‹ค. ์ฃผ์š” ๋‹จ๊ณ„๋Š” ๋‹ค์Œ๊ณผ ๊ฐ™์Šต๋‹ˆ๋‹ค: ์ฃผ์–ด์ง„ WT ์„œ์—ด๊ณผ ๋ฎคํ„ดํŠธ ๋ฆฌ์ŠคํŠธ๋ฅผ ์‚ฌ์šฉํ•˜์—ฌ ๊ฐ ๋‹จ๋ฐฑ์งˆ์— ๋Œ€ํ•œ ๋ฎคํ„ดํŠธ ์„œ์—ด์„ ์ƒ์„ฑํ•ฉ๋‹ˆ๋‹ค. ์ƒ์„ฑ๋œ ๋ฎคํ„ดํŠธ ์„œ์—ด์„ ๋”•์…”๋„ˆ๋ฆฌ์— ์ €์žฅํ•ฉ๋‹ˆ๋‹ค. ๋”•์…”๋„ˆ๋ฆฌ์— ์ €์žฅ๋œ ๋ฎคํ„ดํŠธ ์„œ์—ด์„ FASTA ํ˜•์‹์œผ๋กœ ๋ณ€ํ™˜ํ•˜์—ฌ ์ถœ๋ ฅํ•ฉ๋‹ˆ๋‹ค. ์ฝ”๋“œ๋Š” ์ฃผ๋กœ ๋ฎคํ„ดํŠธ ์„œ์—ด ์ƒ์„ฑ ๋ฐ ๋”•์…”๋„ˆ๋ฆฌ ์กฐ์ž‘, ๊ทธ๋ฆฌ๊ณ  FASTA ํ˜•์‹์œผ๋กœ ๋ณ€ํ™˜ํ•˜๋Š” ํ•จ์ˆ˜๋ฅผ ์ •์˜ํ•˜๊ณ  ํ˜ธ์ถœํ•˜๋Š” ๋ถ€๋ถ„์œผ๋กœ ๊ตฌ์„ฑ๋˜์–ด ์žˆ์Šต๋‹ˆ๋‹ค.
import pandas as pd
seq_Fc_wt = "ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK"
start_num = 118
# ์ฃผ์–ด์ง„ ๋ฎคํ„ดํŠธ ๋ฆฌ์ŠคํŠธ
mutant_list = {
"DLE": ["S239D", "A330L", "I332E"],
"AEFT": ["G236A", "I332E", "H268F", "S324T"],
"GAALIE": ["G236A", "A330L", "I332E"],
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@partrita
partrita / README.md
Last active February 20, 2024 08:46
here's a concise guide on installing and using "whisper" locally for automatic subtitle generation from videos.

0. Requirements

  • video file
  • conda package manager(installed)
  • you

1. How to?

about whisper

@partrita
partrita / README.md
Created February 26, 2024 01:33
Conda with pip

Conda์—์„œ pip ๋ช…๋ น์–ด ์‚ฌ์šฉํ•˜๊ธฐ

์›ํ•˜๋Š” ๋ผ์ด๋ธŒ๋Ÿฌ๋ฆฌ๊ฐ€ conda์— ์—†๋Š” ๊ฒฝ์šฐ pip install์„ ์‚ฌ์šฉํ•ด์•ผ ํ•œ๋‹ค. ๊ทธ๋Ÿฐ๋ฐ pip install๋กœ ํŒจํ‚ค์ง€๋ฅผ ์„ค์น˜ํ•˜๋ฉด conda base ํ™˜๊ฒฝ์— ์„ค์น˜๋œ๋‹ค. ๋”ฐ๋ผ์„œ ๊ฐ€์ƒ ํ™˜๊ฒฝ์— ๋จผ์ € pip๋ฅผ ์„ค์น˜ํ•˜๊ณ  ์ง„ํ–‰ํ•ด์•ผ ํ•œ๋‹ค. ์‚ฌ์‹ค ์ฒ˜์Œ์— ๊ฐ€์ƒํ™˜๊ฒฝ ๋งŒ๋“ค๋•Œ ์•„๋ž˜์ฒ˜๋Ÿผ pip๋ฅผ ์„ค์น˜ํ•˜๋ฉด ์ด๋Ÿฐ ๋ฌธ์ œ๋ฅผ ์‚ฌ์ „์— ๋ฐฉ์ง€ ํ•  ์ˆ˜ ์žˆ๋‹ค.

conda create -n [env_name] python=3.9 pip