Roadmap

This page contains notes for the planned future development of pyani

Index

• Interface

Interface

The current interface for pyani scripts is to call either the average_nucleotide_identity.py or genbank_get_genomes_by_taxon.py scripts with a combination of arguments. For the average_nucleotide_identity.py script in particular there are arguments that either perform a stage in the total analysis, or prevent a stage from executing. I would like to change this interface to a pyani.py COMMAND OPTIONS structure, similar to git and other tools.

More specificially, I would like to enable operations such as:

• pyani.py download -t 931 -o my_organism: download all NCBI assemblies under taxon 931 to the directory my_organism
• pyani.py index my_organism: generate MD5 or other hashes for each genome in the directory my_organism
• pyani.py anim my_organism -o my_organism_ANIm --scheduler SGE: conduct ANIm analysis on the genomes in the directory my_organism
• pyani.py anib my_organism -o my_organism_ANIb --scheduler SGE: conduct ANIb analysis on the genomes in the directory my_organism
• pyani.py render my_organism_ANIm --gmethod seaborn: draw graphical output for the ANIm analysis in the directory my_organism_ANIm
• pyani.py classify my_organism_ANIm: conduct classification analysis of ANIm results in the directory my_organism_ANIm