autoBIGS-cli (0.4.5.dev1+g5ef5b6a)

2025-02-19T16:30:20Z

To install the package using pip, run the following command:

pip install --index-url  autoBIGS-cli

For more information on the PyPI registry, see the documentation.

A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases.

autoBIGS.cli

A command-line interface (CLI) based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST.

This program is simply a command-line interface for autoBIGS.engine.

Features

This CLI is capable of exactly what autoBIGS.engine is capable of:

Import multiple whole genome FASTA files
Fetch the available BIGSdb databases that is currently live and available
Fetch the available BIGSdb database schemas for a given MLST database
Retrieve exact/non-exact MLST allele variant IDs based off a sequence
Retrieve MLST sequence type IDs based off a sequence
Inexact matches are annotated with an asterisk (*)
Output all results to a single CSV

Planned Features for CLI

Specifications of multi-threading capacity
Session authentication for updated database schemas (as required by both PubMLST and Institut Pasteur)

Please refer to autoBIGS.engine for more planned features.

Usage

This CLI can be installed with pip. Please ensure pip is installed. Then:

Run pip install autoBIGS-cli to install the latest version of the CLI for autoBIGS.
Once installation is complete, run autoBIGS --version to test that the installation succeeded (and that you are running the appropriate version).
Run autoBIGS -h to get information on how to get started.

Example

Let's say you have a fasta called seq.fasta which contains several sequences. You know all sequences in seq.fasta are Bordetella pertussis sequences, and you know you have the sequences for the necessary targets of your schema in each of them. You want to retrieve MLST profiles for all of them. This can be done by:

Running autobigs info -l to list all available seqdef databases and find the database associated with Bordetella (you should see one called pubmlst_bordetella_seqdef).
Then, run autobigs info -lschema pubmlst_bordetella_seqdef to get the available typing schemas and their associated IDs. In this example, let's assume we want a normal MLST scheme. In this case, we would pay attention to the number next to MLST (it should be 3).
Then, run autobigs st -h and familiarize yourself with the parameters needed for sequence typing.
Namely, you should find that you will need to run autobigs st seq.fasta pubmlst_bordetella_seqdef 3 output.csv. You can optionally include multiple FASTA files, and --stop-on-fail to stop typing if one of your sequences fail to retrieve any type.
Sit tight, and wait. The output.csv will contain your results once completed.

Versioning

the autoBIGS project follows semantic versioning where the three numbers may be interpreted as MAJOR.MINOR.PATCH.

Note regarding major version 0 (spec item 4), the following adaptation of semantic versioning definition is as follows:

Given x.Y.z, Y is only incremented when a backwards incompatible change is made.
Given x.y.Z, Z is only incremented when a backwards compatible change is made.

Versions of autoBIGS items with a major version number of 0 will introduce numerous changes and patches. As such, changes between such versions should be considered highly variable.

Requires Python: >=3.12

Details

PyPI

ydeng/autoBIGS.cli

2025-02-19 16:30:20 +00:00

0

GPL-3.0-or-later

35 KiB

Assets (2)

autoBIGS.cli-0.4.5.dev1+g5ef5b6a-py3-none-any.whl 18 KiB

autobigs_cli-0.4.5.dev1+g5ef5b6a.tar.gz 17 KiB

Versions (12) View all