corneliusroemer’s gists

corneliusroemer / postgresCustom2.json

Created September 15, 2024 17:08

	{
	"$schema": "https://lnav.org/schemas/format-v1.schema.json",
	"postgres2": {
	"regex": {
	"duration": {
	"pattern": "^(?<timestamp>\\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}\\.\\d{3} UTC) (?<ip>\\d+\\.\\d+\\.\\d+\\.\\d+)\$(?<port>\\d+)\$ (?<session_id>[^ ]+) (?<transaction_id>\\d+) (?<operation>[A-Z]+) ?(?<level>[A-Z]+)?: (?:duration: (?<dur>\\d+\\.\\d+) ms)?(?<body>.*)$"
	}
	},
	"opid-field": "transaction_id",
	"level-field": "level",

corneliusroemer / sitemap.txt

Created August 29, 2024 01:30

	https://pathoplexus.org/
	https://pathoplexus.org/about
	https://pathoplexus.org/about/development-team
	https://pathoplexus.org/about/eb
	https://pathoplexus.org/about/faq
	https://pathoplexus.org/about/governance
	https://pathoplexus.org/about/governance/data-submission
	https://pathoplexus.org/about/governance/eb-guidelines
	https://pathoplexus.org/about/governance/minutes
	https://pathoplexus.org/about/governance/minutes/2024-08-12_PathoplexusEBmeeting.pdf

corneliusroemer / Newick.g4

Created December 19, 2023 01:59

ANTLR4 grammar for parsing Newick trees

	// A Newick grammar based on the specification by Gary Olsen: available at
	// https://phylipweb.github.io/phylip/newick_doc.html The grammar does _not_ include the optional
	// comments as I have not figured out how to include them without adding a lot of `comment?` rules
	// to the grammar whick makes it very slow.

	grammar Newick;

	tree: descendantList rootLabel? branchLength? SEMI;
	descendantList: LPAREN subtree (COMMA subtree)* RPAREN;
	subtree: (descendantList internalNodeLabel? \| leafLabel) branchLength?;

corneliusroemer / constraint_detector.py

Created December 17, 2023 11:31

Script to detect incompatible splits in two newick trees

	import argparse
	from pprint import pp

	from Bio import Phylo


	def get_terminals(clade):
	return frozenset(terminal.name for terminal in clade.get_terminals())

corneliusroemer / nearest_nodes.ndjson

Created December 1, 2023 14:48

Test data to reproduce polars bug

This file has been truncated, but you can view the full file.

	{"seqName":"England/MILK-28D52E2/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"USA/CO-CDPHE-2102374275/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"Wales/PHWC-PGY3IH/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"Turkey/HSGM-F70/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"USA/WI-CDC-QDX31282160/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"Canada/ON-SHL-21-02331/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"France/BRE-IPP48628/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"USA/CA-CDC-LC0396661/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"France/OCC-HCL021227635901/2021","nearestNodes":["B.1.617.2"]}

corneliusroemer / auto-faculty-profile.py

Created September 26, 2023 02:24

Automatically generate faculty profiles using pubmed abstracts and GPT-4, filtering papers for relevance based on author position

	import argparse
	from math import e
	from Bio import Entrez
	import openai

	def search_latest_papers(faculty_name, source="Pubmed", num_papers=5):
	papers_info = []

	if source == "Pubmed":
	Entrez.email = "YOUR_EMAIL@example.com"

corneliusroemer / auto-faculty-profile.py

Created September 25, 2023 23:40

Automatically generate faculty profiles using pubmed abstracts and GPT-4

	import argparse
	from math import e
	from Bio import Entrez
	import openai


	def search_latest_papers(faculty_name, source="Pubmed", num_papers=5):
	abstracts = []

	if source == "Pubmed":

corneliusroemer / gist:3a1dc19e6aa3ab5c94a5ed832a4a2c8e

Created August 8, 2023 14:22

21Ltree20230808

This file has been truncated, but you can view the full file.

corneliusroemer / bf42tree.json

Created April 17, 2023 12:42

This file has been truncated, but you can view the full file.

corneliusroemer / auspice.json

Created March 23, 2023 14:52

Test tree for Auspice PR #1655

This file has been truncated, but you can view the full file.

Cornelius Roemer corneliusroemer