wjs20

#!/usr/bin/env bash

echo $1 | rev | tr TAGC ATCG

wjs20

# reorder manually
import pandas as pd

df = pd.DataFrame({'x': ['low', 'medium', 'high', 'medium']})
df['x'] = df['x'].astype('category')

df['x'] = df['x'].cat.reorder_categories(['low', 'medium', 'high'], ordered=True)


# reorder by another variable

wjs20

#!/usr/bin/env bash
#
#
PS3="Select an option: "
select opt in "Option 1" "Option 2" "Quit"; do
  echo "You picked $opt"
  break
done

wjs20

import pandas as pd
from pathlib import Path

COLSPECS = [
    (0, 6), (6, 11), (12, 16), (16, 17), (17, 20),
    (21, 22), (22, 26), (26, 27), (30, 38), (38, 46),
    (46, 54), (54, 60), (60, 66), (72, 76), (76, 78),
    (78, 80)
]

wjs20

#!/usr/bin/env python
import pyarrow.parquet as pq
import pyarrow as pa
import glob
import sqlite3
import polars as pl
from pathlib import Path
from tqdm import tqdm
import sys

wjs20

#!/usr/bin/env bash
#
# A program to remove protons from pdb files
#
mkdir -p $1-deprotonated

fd -t f -e .pdb . $1 |
    parallel --eta "pdb_delelem -H {} > $1-deprotonated/{/}"

wjs20

IMGT_FRAMEWORK = {
    1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
    21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
    55, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
    87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 118, 119,
    120, 121, 122, 123, 124, 125, 126, 127, 128, 129
}

# Coreset is a minimally varying set of positions (in physical space)

wjs20

Mononoki
Fira Code
Cascadia Code
Monospace
Comic Mono
Agave
Inconsolata
JetBrains Mono
Cousine
Ubuntu Mono

wjs20

#!/usr/bin/env bash
# fasta_converter.sh
#
usage() {
    echo "Usage: $0 [-i input_file.csv] [-o output_file.fasta]"
    echo "  -i : Specify the input file (CSV). If omitted, reads from stdin."
    echo "  -o : Specify the output file (FASTA). If omitted, writes to stdout."
    echo "  -h : Display this help and exit."
    exit 1
}

wjs20

import os
import requests
from concurrent.futures import ThreadPoolExecutor
from urllib.parse import urlparse

def download_urls(url_list, download_dir, max_threads=5):
    if not os.path.exists(download_dir):
        os.makedirs(download_dir)
    
    def download_url(url):