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Cornelius Roemer corneliusroemer

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@corneliusroemer
corneliusroemer / add-branch-labels.py
Created February 22, 2023 19:49
Script to add node data as branch label
import argparse
import json
def extract_attribute(node_data, attribute: str) -> dict[str, str]:
data = {}
for name, node in node_data["nodes"].items():
if attribute in node:
data[name] = node[attribute]
return data
@corneliusroemer
corneliusroemer / auspice.json
Created March 8, 2023 18:25
Tree with log_priors
This file has been truncated, but you can view the full file.
{"version":"v2","meta":{"title":"SARS-CoV-2 phylogeny","updated":"2023-03-08","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":{"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 / auspice.json
Created March 9, 2023 17:50
Tree with log_priors, floats unquoted
This file has been truncated, but you can view the full file.
{"version":"v2","meta":{"title":"SARS-CoV-2 phylogeny","updated":"2023-03-08","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":{"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 / 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
@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 / 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.
{"version":"v2","meta":{"title":"SARS-CoV-2 phylogeny","updated":"2023-03-15","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 / json_diffs.md
Created March 16, 2023 17:25
JSON diff tool
@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 / 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 / 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":{"