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
2 maintainers
Metadata
2 maintainers
Release files for rmlst-cli 1.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| rmlst_cli-1.1-py3-none-any.whl | Python 3 | none | any | Details for rmlst_cli-1.1-py3-none-any.whl |
Total release size: 22.7 kB
Release files / rmlst_cli-1.1.tar.gz
| Download URL | rmlst_cli-1.1.tar.gz |
|---|---|
| Size | 10.0 kB |
| Tags | Source |
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| Size | 12.8 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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twine/6.1.0 CPython/3.13.12
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Signed by GitHub Actions, verified by PyPI on Jun 13, 2026.
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