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St3451 merged 1 commit into from
May 26, 2026
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docs: review fixes + relocate get_regions_file.py #97

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4 changes: 2 additions & 2 deletions docs/run_input_output.md
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Expand Up @@ -117,7 +117,7 @@ To compute the mutation profile with BGSignature two main files are required:

##### Create the Regions File

A small helper script ([tools/preprocessing/get_regions_file.py](../tools/preprocessing/get_regions_file.py)) generates the regions file via BGReference.
A small helper script ([tools/mut_profile/get_regions_file.py](../tools/mut_profile/get_regions_file.py)) generates the regions file via BGReference.

1. Install BGReference:
```
Expand All @@ -126,7 +126,7 @@ A small helper script ([tools/preprocessing/get_regions_file.py](../tools/prepro

2. Run the helper from the repo root:
```
python tools/preprocessing/get_regions_file.py hg38 3 > hg38_wg_regions.tsv
python tools/mut_profile/get_regions_file.py hg38 3 > hg38_wg_regions.tsv
```
Supported genomes: `hg18`, `hg19`, `hg38`, `mm10`, `mm39`. The first argument is the genome build; the second is the k-mer size (typically `3` for trinucleotide contexts).

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0 tools/preprocessing/get_regions_file.py → tools/mut_profile/get_regions_file.py
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