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autoBIGS.cli/README.md

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autoMLST.CLI

A command-line interface based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV.

This program is simply a command-line interface for autoMLST.Engine.

Features

This CLI is capable of exactly what autoMLST.Engine is capable of:

  • Import multiple 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
  • Output all results to a single CSV

Usage

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

  1. Run pip install automlst-cli to install the latest version of the CLI for autoMLST.

  2. Once installation is complete, run automlst --version to test that the installation succeeded (and that you are running the appropriate version).

  3. Run automlst -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:

  1. Running automlst info -l to list all available seqdef databases and find the database associated with Bordetella (you should see one called pubmlst_bordetella_seqdef).

  2. Then, run automlst 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).

  3. Then, run automlst st -h and familiarize yourself with the parameters needed for sequence typing.

  4. Namely, you should find that you will need to run automlst st seq.fasta pubmlst_bordetella_seqdef 3 output.csv. You can optionally include multiple FASTA files, and/or --exact to only retrieve exact sequence types, and/or --stop-on-fail to stop typing if one of your sequences fail to retrieve any type.

  5. Sit tight, and wait. The output.csv will contain your results once completed.