From 17f2858c9c10e3e9885b097e990062379a938dc7 Mon Sep 17 00:00:00 2001 From: cdbope Date: Thu, 6 Jun 2024 09:37:08 +0200 Subject: [PATCH] update readme and min number of signature when using --signature-names option --- README.rst | 5 ++++- mutational_starsign/cli.py | 7 ++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/README.rst b/README.rst index 45bf3439..01caf59a 100644 --- a/README.rst +++ b/README.rst @@ -5,7 +5,7 @@ StarSignDNA Mutation signature analysis package ----------------------------------- -* Free software: MIT license +* Free software: `MIT license `_ * Documentation: Link to be provided Features @@ -21,6 +21,9 @@ To install StarSign, run this command in your terminal:: 3. cd StarSigndna-master/ 4. pip install -e . +Alternatively, you can install the package directly from PyPi:: + + pip install starsigndna Getting started --------------- diff --git a/mutational_starsign/cli.py b/mutational_starsign/cli.py index b748e06b..32a4d746 100644 --- a/mutational_starsign/cli.py +++ b/mutational_starsign/cli.py @@ -450,13 +450,10 @@ def read_counts(matrix_file): M = pd.read_csv(matrix_file, delimiter='\t') return M -def filter_signatures_old(S, signature_names): - S = S.loc[signature_names] - return S def filter_signatures(S, signature_names): - if len(signature_names) < 5: - raise ValueError("You must select at least 5 signature names.") + if len(signature_names) < 3: + raise ValueError("You must select at least 3 signature names.") S = S.loc[signature_names] return S