Bioscripts

A collection of Python scripts developed during my PhD for automating small, repetitive bioinformatics tasks. These tools primarily interface with NCBI/EMBL, process genomic data, and parse output from common bioinformatics tools.

Requirements

• Python 3.10+
• BioPython
• Pandas

Scripts

antiSMASH (antismash/)

Tools for processing antiSMASH biosynthetic gene cluster (BGC) analysis results.

Script	Description
count_regions.py	Count BGC regions across multiple antiSMASH result directories
tabulate_regions.py	Tabulate BGC regions with detailed metadata including KnownClusterBlast hits

Fuzznuc (fuzznuc/)

Tools for working with EMBOSS fuzznuc motif search results.

Script	Description
metadata2table.py	Find genes near fuzznuc motif hits and extract metadata from NCBI GenBank
merge_gbk.py	Merge fuzznuc results into a GenBank genome file as misc_binding features

Miscellaneous (misc/)

General-purpose utilities for NCBI data retrieval and processing.

Script	Description
get_organism_name_from_reference.py	Extract organism names from NCBI nucleotide accessions
reference2assembly.py	Convert NCBI nucleotide accessions to assembly accessions

Usage

All scripts include a command-line interface. Use -h or --help for usage information:

python antismash/count_regions.py -h
python fuzznuc/metadata2table.py -h

Most scripts support multithreading via --threads and NCBI scripts accept --email and --api-key for Entrez queries.

License

See LICENSE for details.