From 3fa10293933184097b09a46b291ac96db7781db8 Mon Sep 17 00:00:00 2001 From: Valentin Zulkower Date: Wed, 6 Nov 2024 17:37:58 -0500 Subject: [PATCH] removed some final commas in function parameters --- dnachisel/SequencePattern/MotifPssmPattern.py | 19 ++++--------------- 1 file changed, 4 insertions(+), 15 deletions(-) diff --git a/dnachisel/SequencePattern/MotifPssmPattern.py b/dnachisel/SequencePattern/MotifPssmPattern.py index 9916b9b..1b8cef6 100644 --- a/dnachisel/SequencePattern/MotifPssmPattern.py +++ b/dnachisel/SequencePattern/MotifPssmPattern.py @@ -30,12 +30,7 @@ class MotifPssmPattern(SequencePattern): sequence(s) with the absolute highest possible score". """ - def __init__( - self, - pssm, - threshold=None, - relative_threshold=None, - ): + def __init__(self, pssm, threshold=None, relative_threshold=None): if not isinstance(pssm, Bio.motifs.Motif): raise ValueError( f"Expected PSSM type of `Bio.motifs.Motif`, but {type(pssm)} was passed" @@ -74,9 +69,7 @@ def find_matches_in_string(self, sequence): # sequence, threshold=self.threshold, both=False # ) indices = find_pssm_matches_with_numpy( - pssm_matrix=self.pssm_matrix, - sequence=sequence, - threshold=self.threshold, + pssm_matrix=self.pssm_matrix, sequence=sequence, threshold=self.threshold ) return [(i, i + self.size, 1) for i in indices] @@ -121,9 +114,7 @@ def from_sequences( motif.name = name pssm = motif return MotifPssmPattern( - pssm=pssm, - threshold=threshold, - relative_threshold=relative_threshold, + pssm=pssm, threshold=threshold, relative_threshold=relative_threshold ) @classmethod @@ -172,9 +163,7 @@ def list_from_file( return [ MotifPssmPattern( - pssm, - threshold=threshold, - relative_threshold=relative_threshold, + pssm, threshold=threshold, relative_threshold=relative_threshold ) for pssm in motifs_list ]