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@corneliusroemer
corneliusroemer / json_diffs.md
Created March 16, 2023 17:25
JSON diff tool

Use jsondiffpatch not json-diff jsondiffpatch is much faster json-diff took >30s (couldn't bother waiting anymore) what jsondiffpatch did in <1s https://github.com/benjamine/jsondiffpatch

npm install -g jsondiffpatch
@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 / 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
@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 / 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 / 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 / pyproject.toml
Created November 11, 2022 14:01
[tool.poetry]
name = "nwkfmt"
version = "0.1.0"
description = "Simple Newick tree validator and formatter"
authors = ["Cornelius Roemer <cornelius.roemer@gmail.com>"]
readme = "README.md"
[tool.poetry.scripts]
greet = "nwkfmt.cli:main"
@corneliusroemer
corneliusroemer / Biontech_Moderna_Wuhan_aa.fasta
Created January 24, 2022 20:18
Aligned nucleotide sequences from https://github.com/NAalytics/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273/blob/main/Figure1Figure2_032321.fasta
>MN908947 (Wuhan-Hu-1/2019)
TTELLFLVMFLLTTKRTMFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLND
@corneliusroemer
corneliusroemer / virus.json
Created January 14, 2022 17:49
{
"nucMutLabelMap": {
"A10195G": [
"20I (Alpha, V1)"
],
"A10317G": [
"21J (Delta)"
],
"A10323G": [
"21J (Delta)",