Small single-purpose Python scripts written during PhD and paper work on antimicrobial resistance and bacterial phylogenomics. They are kept here because they turned out to be useful more than once — not because they are a package. There is no installer and no test suite.
Read before running: several scripts still carry the absolute paths of the machine they were written on (
/home/analysis/Desktop/...). Open the file and edit the paths at the top before use. Moving those to command-line arguments is the obvious next step for any script you find yourself reusing.
| Script | Does |
|---|---|
ALNtoFASTA_converter.py |
Clustal .aln → FASTA (Biopython AlignIO) |
phy_converter.py |
Clustal .aln → PHYLIP, for tools that insist on it |
converter.py |
PHYLIP → FASTA. Imports Bio.Alphabet, removed in Biopython 1.78 — needs updating before it runs on a current install |
check_length.py |
Flags sequences in an alignment whose length differs from the rest — the usual reason a downstream tool refuses the file |
| Script | Does |
|---|---|
gene_platter.py |
Dash app: interactive time-series view of accessory and core genes |
abscenary.py |
Dash app: multi-gene presence/absence viewer from gene_presence_absence.csv (Roary / Panaroo output), with warnings for hypothetical proteins |
gene_mapper.py |
Streamlit app: gene presence mapped onto a phylogenetic tree |
beast_visualiser.py |
Plots BEAST .log traces — parameter distributions and convergence |
gorsel.py |
Heatmap of chromosomal AMR genes from a CSV |
variant_statisics.py |
Aggregates bcftools stats output across many VCFs into summary plots |
Untitled.ipynb — scratch work, kept for reference.
Nothing is pinned. Between them the scripts want:
pip install biopython pandas matplotlib seaborn plotly dash streamlitRun a Dash or Streamlit app with python gene_platter.py / streamlit run gene_mapper.py.
This repository used to be called python_scipts (typo included). GitHub
redirects the old URL, so existing clones and links keep working.