Cornelius Roemer corneliusroemer
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| {"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
/ add-branch-labels.py
Created
February 22, 2023 19:49
Script to add node data as branch label
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| 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
/ pyproject.toml
Created
November 11, 2022 14:01
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| [tool.poetry] | |
| name = "nwkfmt" | |
| version = "0.1.0" | |
| description = "Simple Newick tree validator and formatter" | |
| authors = ["Cornelius Roemer <[email protected]>"] | |
| readme = "README.md" | |
| [tool.poetry.scripts] | |
| greet = "nwkfmt.cli:main" |
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
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| >MN908947 (Wuhan-Hu-1/2019) | |
| TTELLFLVMFLLTTKRTMFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLND |
corneliusroemer
/ virus.json
Created
January 14, 2022 17:49
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| { | |
| "nucMutLabelMap": { | |
| "A10195G": [ | |
| "20I (Alpha, V1)" | |
| ], | |
| "A10317G": [ | |
| "21J (Delta)" | |
| ], | |
| "A10323G": [ | |
| "21J (Delta)", |
corneliusroemer
/ reparam_bug.ipynb
Created
December 30, 2021 11:34
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| // Future versions of Hyper may add additional config options, | |
| // which will not automatically be merged into this file. | |
| // See https://hyper.is#cfg for all currently supported options. | |
| module.exports = { | |
| config: { | |
| // choose either `'stable'` for receiving highly polished, | |
| // or `'canary'` for less polished but more frequent updates | |
| updateChannel: 'stable', |
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| jq 'if .topic == "devices_overview" then .timestamp = (.timestamp * 1000 | round | tostring) else . end' <out |
corneliusroemer
/ diffscript
Created
April 21, 2020 15:05
Comparing text files, only changed lines shown, changed words color highlighted
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| diff -U 0 gry gryold | wdiff -d | colordiff |
corneliusroemer
/ findgunzip.sh
Last active
April 16, 2020 14:46
Extract and concatenate all .gz files in all subdirectories into a new text file without touching the original files
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| find . -name '*.gz' -exec gzip -ckd {} + > test.txt |