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Merge pull request #67 from michaelmeuli/patch-2
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Update README.md
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jodyphelan authored Aug 29, 2024
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Expand Up @@ -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.
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