rmlst-cli 1.1

rmlst-cli is a simple tool to use the rMLST API through the command line.

rmlst-cli

rmlst-cli is a simple tool to use the rMLST API through the command line.

Install

pip install rmlst-cli
# or
uv tool install rmlst-cli
# or
conda install -c bioconda rmlst-cli
# or
pixi add -c bioconda rmlst-cli

Quickstart

Single FASTA file:

rmlst -f sample.fasta

Directory of FASTA files:

rmlst -d ./fastas/ -O ./results/

Output modes

• Full JSON (default):

  rmlst -f sample.fasta
  

• Species only (two columns: species and support):

  rmlst -f sample.fasta --species-only
  # With custom headers
  rmlst -f sample.fasta --species-only="Species Support"
  

Examples

Trim to 5000 contigs:

rmlst -f large.fasta --trim-to-5000

Graceful failure (continue on error):

rmlst -d ./fastas/ --graceful

Exit codes

Code	Meaning
0	Success
1	Unexpected error
2	Input/usage error (invalid FASTA, empty dir, etc.)
3	Too many contigs (>5000) without --trim-to-5000
4	Network error after retries
5	HTTP error or invalid JSON
7	Filesystem error
130	Interrupted (Ctrl-C)

Python API usage

from rmlst_cli import api

# Single file
try:
    result = api.identify("sample.fasta")
    print(result)
except Exception as e:
    print(f"Error: {e}")

# Directory
for basename, result in api.identify_dir("./fastas/", graceful=True):
    print(f"{basename}: {result}")

# Extract species
from rmlst_cli.formats import extract_species, extract_species_and_support
species = extract_species(result)  # Comma-separated string
species_names, support_values = extract_species_and_support(result)  # Separate strings