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.
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 `autobigs 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 `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`).
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 `--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.
## Versioning
the autoBIGS project follows [semantic versioning](https://semver.org/) where the three numbers may be interpreted as MAJOR.MINOR.PATCH.
Note regarding major version 0 ([spec item 4](https://semver.org/#spec-item-4)), the following adaptation of semantic versioning definition is as follows:
1. Given x.Y.z, Y is only incremented when a backwards incompatible change is made.
2. 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.
