portfolio

A collection of scripts and workflows that folks on the internet might find useful.

anvio accessory functions

I highly recommend anvio for pretty much anything related to microbial ‘omics.

extract-gene-functions.py

Gene functions can be exported from anvio contigs databases using the anvio command anvi-export-functions.
Maybe you have many contigs dbs (each corresponding to genomes or MAGs) that you want to export gene functions from. This simple python script exports genes from multiple sources and binds them into one text file, adding a column corresponding to the source database.

import-whokaryote-gene-calls-to-anvio.py

Whokaryote is a tool for classifying contigs by domain of origin (eukaryotic vs prokaryotic). By default, it will perform gene calling on contigs using Prodigal. Anvio users with samples containing both bacteria/archaea and eukaryotes may choose to run this step before generating a contigs database, but there’s no need to rerun prokaryotic gene calling again. import-whokaryote-gene-calls-to-anvio.py reformats the file output by whokaryote (called contigs_genes.gff) into an external_gene_calls.txt that can be imported into an anvio contigs database. This might work with other .gff output formats but I haven’t tested it extensively. Additional functionality could also use the contigs_proteins.faa output file so anvi-gen-contigs-db doesn’t need to bother with translating.