Skip to content

Instantly share code, notes, and snippets.

View corneliusroemer's full-sized avatar

Cornelius Roemer corneliusroemer

247 followers · 226 following
View GitHub Profile
@corneliusroemer
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
corneliusroemer / gist:3a1dc19e6aa3ab5c94a5ed832a4a2c8e
Created August 8, 2023 14:22
21Ltree20230808
This file has been truncated, but you can view the full file.
{"version":"v2","meta":{"title":"SARS-CoV-2 phylogeny","updated":"2023-08-08","build_url":"https://github.com/neherlab/nextclade_data_workflows","maintainers":[{"name":"Cornelius Roemer","url":"https://neherlab.org"},{"name":"Richard Neher","url":"https://neherlab.org"}],"display_defaults":{"color_by":"clade_membership","distance_measure":"div","map_triplicate":false,"branch_label":"clade","transmission_lines":false},"genome_annotations":{"E":{"end":26472,"seqid":"defaults/reference_seq.gb","start":26245,"strand":"+","type":"CDS"},"M":{"end":27191,"seqid":"defaults/reference_seq.gb","start":26523,"strand":"+","type":"CDS"},"N":{"end":29533,"seqid":"defaults/reference_seq.gb","start":28274,"strand":"+","type":"CDS"},"ORF1a":{"end":13468,"seqid":"defaults/reference_seq.gb","start":266,"strand":"+","type":"CDS"},"ORF1b":{"end":21555,"seqid":"defaults/reference_seq.gb","start":13468,"strand":"+","type":"CDS"},"ORF3a":{"end":26220,"seqid":"defaults/reference_seq.gb","start":25393,"strand":"+","type":"CDS"},"ORF6":
@corneliusroemer
corneliusroemer / bf42tree.json
Created April 17, 2023 12:42
This file has been truncated, but you can view the full file.
{ "version": "v2", "meta": { "title": "Subtree with Japan\/PG-462868\/2023|EPI_ISL_17243060|2023-02-28 and 51 other uploaded samples", "description": "Dataset generated by [UShER web interface](https:\/\/genome.ucsc.edu\/cgi-bin\/hgPhyloPlace) using the [usher](https:\/\/github.com\/yatisht\/usher\/) program. If you have metadata you wish to display, you can now drag on a CSV file and it will be added into this view, [see here](https:\/\/docs.nextstrain.org\/projects\/auspice\/en\/latest\/advanced-functionality\/drag-drop-csv-tsv.html) for more info.", "panels": [ "tree", "entropy"] , "display_defaults": { "branch_label": "aa mutations", "color_by": "pango_lineage_usher"} , "colorings": [ { "key": "userOrOld", "title": "Sample type", "type": "categorical", "scale": [ [ "uploaded sample", "#CC0000"] , [ "GISAID and\/or public", "#000000"] ] } , { "key": "gt", "title": "Genotype", "type": "categorical"} , { "key": "pango_lineage", "title": "Pango lineage", "type": "categorical"} , { "key": "Nextstrain_clade",
@corneliusroemer
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.
{"version":"v2","meta":{"title":"SARS-CoV-2 phylogeny","updated":"2023-03-22","build_url":"https://github.com/neherlab/nextclade_data_workflows","maintainers":[{"name":"Cornelius Roemer","url":"https://neherlab.org"},{"name":"Richard Neher","url":"https://neherlab.org"}],"display_defaults":{"color_by":"clade_membership","distance_measure":"div","map_triplicate":false,"branch_label":"clade","transmission_lines":false},"genome_annotations":{"nuc":{"end":29903,"start":1,"strand":"+","seqid":"defaults/reference_seq.gb","type":"source"},"E":{"end":26472,"seqid":"defaults/reference_seq.gb","start":26245,"strand":"+","type":"CDS"},"M":{"end":27191,"seqid":"defaults/reference_seq.gb","start":26523,"strand":"+","type":"CDS"},"N":{"end":29533,"seqid":"defaults/reference_seq.gb","start":28274,"strand":"+","type":"CDS"},"ORF1a":{"end":13468,"seqid":"defaults/reference_seq.gb","start":266,"strand":"+","type":"CDS"},"ORF1b":{"end":21555,"seqid":"defaults/reference_seq.gb","start":13468,"strand":"+","type":"CDS"},"ORF3a":{"
@corneliusroemer
corneliusroemer / virus_properties.json
Created March 21, 2023 00:40
Virus properties using sites 100-29720 for placement
{
"schemaVersion": "1.10.0",
"placementMaskRanges": [{"begin":0,"end":100},{"begin":29720,"end":30000}],
"nucMutLabelMap": {
"174T": [
"20H"
],
"204T": [
"20E"
],
@corneliusroemer
corneliusroemer / virus_properties.json
Created March 21, 2023 00:29
Virus properties for placement of 100-10k only
{
"schemaVersion": "1.10.0",
"placementMaskRanges": [{"begin":0,"end":100},{"begin":10700,"end":30000}],
"nucMutLabelMap": {
"174T": [
"20H"
],
"204T": [
"20E"
],
@corneliusroemer
corneliusroemer / json_diffs.md
Created March 16, 2023 17:25
JSON diff tool
@corneliusroemer
corneliusroemer / gist:9e18bd1063aec873f654d1d7b170dd09
Created March 15, 2023 21:49
Nextclade SC2 ref tree with priors - 2023-03-15
This file has been truncated, but you can view the full file.
@corneliusroemer
corneliusroemer / XP.fasta.txt
Created March 13, 2023 08:48
Fasta for visual bug repro (Nextclade)
>XP
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT
GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT
CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC
TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
TGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC
ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG
AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG
CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA
ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT
@corneliusroemer
corneliusroemer / subprocess_latency.md
Last active March 10, 2023 09:19
Bash subprocess spawn latency

Latency to start a subprocess in bash

Q: How long does it roughly take to spawn a subprocess in bash? A: Around 1 millisecond

Method

$ time for i in {0..1000} ; do $(echo "1") 2&>1 >/dev/null; done