From d0d350dae7c8bf16e2f115f26a275385ef46d3e1 Mon Sep 17 00:00:00 2001 From: Michael Meuli Date: Wed, 28 Aug 2024 10:00:34 +0200 Subject: [PATCH] Update README.md Rename tbdb.csv to mutations.csv --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 53a530a..5051843 100644 --- a/README.md +++ b/README.md @@ -18,13 +18,13 @@ If you think a mutation should be removed or added please raise and issue [here] If you want to help curate the library, leave a comment [here](https://github.com/jodyphelan/tbdb/issues/4). #### Adding/removing mutations -Mutations can be added by submitting a pull request on a branch modified `tbdb.csv` file. If that previous sentence made no sense to you then you can suggest a change using an [issue](https://github.com/jodyphelan/tbdb/issues) and we will try help. On submitting a pull request the `tbdb_bot` will automatically calculate the confidence of the mutations in question and submit the results as a comment on the pull request (like [this](https://github.com/jodyphelan/tbdb/pull/5)). All `tbdb_bot` checks should pass, at least two reviews should be requested and upon review can be merged into the master branch +Mutations can be added by submitting a pull request on a branch modified `mutations.csv` file. If that previous sentence made no sense to you then you can suggest a change using an [issue](https://github.com/jodyphelan/tbdb/issues) and we will try help. On submitting a pull request the `tbdb_bot` will automatically calculate the confidence of the mutations in question and submit the results as a comment on the pull request (like [this](https://github.com/jodyphelan/tbdb/pull/5)). All `tbdb_bot` checks should pass, at least two reviews should be requested and upon review can be merged into the master branch ## How does it work? -The mutations are listed in [tbdb.csv](https://github.com/jodyphelan/tbdb/blob/master/tbdb.csv). These are parsed by `parse_db.py` to generate the json formatted database used by TBProfiler along with a few more files. Mutations can be removed and added from tbdb.csv and a new library can be built using `parse_db.py`. +The mutations are listed in [mutations.csv](https://github.com/jodyphelan/tbdb/blob/master/mutations.csv). These are parsed by `parse_db.py` to generate the json formatted database used by TBProfiler along with a few more files. Mutations can be removed and added from mutations.csv and a new library can be built using `parse_db.py`. -#### tbdb.csv +#### mutations.csv This is a CSV file which must contain the following column headings: 1. **Gene** - These can be the gene names (e.g. *rpoB*) or locus tag (e.g. *Rv0667*). 2. **Mutation** - These must follow the [hgvs nomenclature](http://varnomen.hgvs.org/). More info down below.