39 lines
2.4 KiB
Markdown
39 lines
2.4 KiB
Markdown
# autoBIGS.CLI
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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.
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This program is simply a command-line interface for [autoBIGS.Engine](https://pypi.org/project/autoBIGS.engine).
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## Features
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This CLI is capable of exactly what [autoBIGS.Engine](https://pypi.org/project/autoBIGS.engine) is capable of:
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- Import multiple FASTA files
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- Fetch the available BIGSdb databases that is currently live and available
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- Fetch the available BIGSdb database schemas for a given MLST database
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- Retrieve exact/non-exact MLST allele variant IDs based off a sequence
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- Retrieve MLST sequence type IDs based off a sequence
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- Output all results to a single CSV
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## Usage
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This CLI can be installed with `pip`. Please ensure [pip is installed](https://pip.pypa.io/en/stable/installation/). Then:
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1. Run `pip install autoBIGS-cli` to install the latest version of the CLI for autoBIGS.
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2. Once installation is complete, run `autoBIGS --version` to test that the installation succeeded (and that you are running the appropriate version).
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3. Run `autoBIGS -h` to get information on how to get started.
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### Example
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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:
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1. 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`).
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2. 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`).
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3. Then, run `autobigs st -h` and familiarize yourself with the parameters needed for sequence typing.
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4. 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/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.
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5. Sit tight, and wait. The `output.csv` will contain your results once completed. |