From e0a6f05431cdb34fd023f4c0e71bcb9b8d6139aa Mon Sep 17 00:00:00 2001 From: St3451 Date: Wed, 27 May 2026 01:12:16 +0200 Subject: [PATCH] docs: update paths in README for regions file script and add new script for mutation profile --- docs/run_input_output.md | 4 ++-- tools/{preprocessing => mut_profile}/get_regions_file.py | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename tools/{preprocessing => mut_profile}/get_regions_file.py (100%) diff --git a/docs/run_input_output.md b/docs/run_input_output.md index 208e413..297d404 100644 --- a/docs/run_input_output.md +++ b/docs/run_input_output.md @@ -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: ``` @@ -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). diff --git a/tools/preprocessing/get_regions_file.py b/tools/mut_profile/get_regions_file.py similarity index 100% rename from tools/preprocessing/get_regions_file.py rename to tools/mut_profile/get_regions_file.py