diff --git a/README.md b/README.md index 8d3e6fa..13e291a 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,25 @@ -# autoBIGS.CLI +# autoBIGS.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. +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](https://pypi.org/project/autoBIGS.engine). +This program is simply a command-line interface for [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine). ## Features -This CLI is capable of exactly what [autoBIGS.Engine](https://pypi.org/project/autoBIGS.engine) is capable of: -- Import multiple FASTA files +This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/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 - 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](https://pypi.org/project/autoBIGS.engine) for more planned features. + ## Usage This CLI can be installed with `pip`. Please ensure [pip is installed](https://pip.pypa.io/en/stable/installation/). Then: