theosanderson

#!/usr/bin/env python3
import subprocess
import tempfile
import gzip
from pathlib import Path
from Bio import SeqIO

def read_fasta_headers(fasta_file):
    headers = []
    with gzip.open(fasta_file, 'rt') as f:

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(A,B,C,(D,E))

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apiVersion: argoproj.io/v1alpha1
kind: Application
metadata:
  name: reverse-proxy
  namespace: argocd
spec:
  project: default
  source:
    repoURL: https://charts.bitnami.com/bitnami
    targetRevision: 15.1.1

theosanderson

import { useEffect, useRef, useState } from 'react';

export default function LargeComponent() {
  const scrollRef = useRef(null);
  const trackRef = useRef(null);
  const [scrollLeft, setScrollLeft] = useState(0);
  const [maxScroll, setMaxScroll] = useState(0);
  const [handleWidth, setHandleWidth] = useState(0);
  const [dragging, setDragging] = useState(false);
  const [startX, setStartX] = useState(0);

theosanderson

Women in the History of Antimicrobial Development March 15, 2024

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Women working in a Penicillin factory. Women working in a Penicillin factory. Source: Wikimedia Commons

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{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "type": "object",
  "properties": {
    "name": {
      "type": "string",
      "default": "Loculus",
      "description": "The name of the Loculus instance"
    },
    "logo": {

theosanderson

Okay, I need to write a story using only the vowel 'o'. Let me start by brainstorming possible words. Words with 'o' as the only vowel. Hmm. Let's see. First, the characters. Maybe a protagonist named Tom? Wait, no, 'Tom' has 'o' as the vowel. That works. Or maybe 'Bob'? Yes, Bob is good. Let's go with Bob. Now, setting. Maybe a small town? 'Town' is okay. Or a forest? 'Woods' has 'o' and 'o', so that's good.

Plot: Bob needs to solve a problem. Maybe he's looking for something. A lost dog? 'Dog' works. So Bob's dog, maybe named Spot? No, 'Spot' has 'o' as the vowel. Wait, 'Spot' has an 'o' and a 'o'? No, 'S' 'p' 'o' 't'—only 'o' as vowel. So Spot is okay. So Bob's dog Spot is lost. He goes to look for him. Maybe he goes through the woods, meets a fox? 'Fox' is good. The fox helps him. Then they find Spot. But how to structure sentences without other vowels.

Let me list some words. Nouns: Bob, dog, Spot, fox, log, rock, pond, frog, box, sock, clock, shop, top, fog, moss, lot, job, cot, lock, drop, plot, trot

theosanderson

-- Create the test table
CREATE TABLE table_name (
    id SERIAL PRIMARY KEY,
    warnings JSONB
);

-- Insert test data with the original JSON structure
INSERT INTO table_name (warnings) VALUES (
    '[
        {

theosanderson

# Example of how to run: tar -xJOf sequences_fasta_2024_04_25.tar.xz sequences.fasta | python translate.py | pv -l | zstd > seqs.fa.zst
import sys
import tarfile
import pandas as pd

def load_virus_to_accession_dict(tar_path):
    """ Load the virus to accession ID dictionary from a tar.xz file containing a .tsv. """
    with tarfile.open(tar_path, 'r:xz') as tar:
        # Find the tsv file within the archive, assuming there's only one .tsv
        tsv_file = [member for member in tar.getmembers() if member.name.endswith('.tsv')][0]

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LOCUS       MN908947               29903 bp ss-RNA     linear   VRL 18-MAR-2020
DEFINITION  Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,
            complete genome.
ACCESSION   MN908947
VERSION     MN908947.3
KEYWORDS    .
SOURCE      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
  ORGANISM  Severe acute respiratory syndrome coronavirus 2
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae;