Björn Johansson BjornFJohansson
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BjornFJohansson
/ gist:73ad364ac5617dd7d8b4c3df99bced1c
Last active
November 16, 2025 16:21
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| This is the assumed sequence: https://www.ncbi.nlm.nih.gov/nuccore/U25676.1 | |
| Pydnaweb PCR simulation with original primers: | |
| --- | |
| limit: 13 | |
| --- | |
| # pcr | |
| | Component | Name | Size | Seguid | | |
| |-------------|----------------|--------|--------------------------------------| |
BjornFJohansson
/ remove_import_aliases_in_pydna.py
Created
November 4, 2025 05:30
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| #!/usr/bin/env python3 | |
| """ | |
| Clean underscored aliases while preserving original line breaks/spacing. | |
| Rules | |
| ----- | |
| 1) from X import Name as _Name -> from X import Name (and _Name → Name) | |
| 2) import pkg as _pkg -> import pkg (and _pkg → pkg) | |
| 3) import networkx as _nx -> import networkx as nx (and _nx → nx) |
BjornFJohansson
/ pre-commit.sh
Last active
June 7, 2024 04:32
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| #!/usr/bin/bash | |
| # | |
| # Git pre-commit hook for obsidian.ms or other collections of markdown files. | |
| # This hook works with obsidian-git https://github.com/denolehov/obsidian-git | |
| # | |
| # An hook script to verify what is about to be committed. | |
| # This script is called by "git commit" with no arguments. | |
| # The hook should exit with non-zero status after issuing an appropriate message if it wants to stop the commit. | |
| # | |
| # Usage: Remove the .sh file extension when you put the script in your hooks folder! |
BjornFJohansson
/ amc-txt.lang
Created
March 20, 2024 14:50
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <!-- | |
| Copyright (C) 2011-2017 Alexis Bienvenue <[email protected]> | |
| This file is part of Auto-Multiple-Choice | |
| Auto-Multiple-Choice is free software: you can redistribute it | |
| and/or modify it under the terms of the GNU General Public License | |
| as published by the Free Software Foundation, either version 2 of |
BjornFJohansson
/ join_pdfs.py
Created
January 19, 2024 17:25
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| #!/home/bjorn/miniforge3/envs/bjorn311/bin python3 | |
| # -*- coding: utf-8 -*- | |
| # https://pdfstandalone.com/en/merge-pdf | |
| import sys | |
| from pathlib import Path | |
| from borb.pdf.document.document import Document | |
| from borb.pdf.pdf import PDF | |
| from tqdm import tqdm | |
| script, *cliarg = sys.argv |
BjornFJohansson
/ javascript_force.ipynb
Created
January 2, 2024 13:15
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BjornFJohansson
/ wikidpad-to-obsidian.py
Last active
July 29, 2025 10:19
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| from pathlib import Path | |
| import urllib | |
| import re, os | |
| from urllib.parse import urlparse | |
| from string import punctuation | |
| # I used this script in 2023 to convert a wikidpad wiki into a Obsidian.md wiki | |
| # The wikidpad wiki has to be in the "original sqlite" format ie a collection of text files | |
| # The script was run and tweaked and was not run or tested on more than one wiki. | |
| # If you use this, be sure to run this script on a copy of the files as the files are modified |
BjornFJohansson
/ banana-oil-sucrose.ipynb
Created
October 3, 2023 16:26
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BjornFJohansson
/ Escher_Introduction.ipynb
Created
September 20, 2023 14:07
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BjornFJohansson
/ fcs_to_csv.py
Last active
June 23, 2023 14:16
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| # Flow Cytometry Standard file format --> csv | |
| # https://stackoverflow.com/questions/70348405/how-to-convert-lmd-file-to-csv-flow-cytometry-data | |
| # https://pypi.org/project/fcsparser/ | |
| """ | |
| This script collects all files in the same directory as the script (or cwd) with | |
| the file ending "fcs". These files are assumed to be in the Flow Cytometry Standard file format | |
| anhd converted to CSV using pandas, and fcsparser. To install requirements: | |
| pip install fcsparser pandas |
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