From 032af379bd8355e658a3ecf644a7356a8e3c3af4 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 19:33:28 +0200 Subject: [PATCH] ci: fix static code analysis --- scripts/mirna_quantification.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/scripts/mirna_quantification.py b/scripts/mirna_quantification.py index ef29e8c..0d0def4 100755 --- a/scripts/mirna_quantification.py +++ b/scripts/mirna_quantification.py @@ -1,5 +1,7 @@ #!/usr/bin/env python +# pylint: disable=line-too-long + """Quantify miRNAs and corresponding isomiRs. Read the input SAM file, calculate the contribution sum of the intersecting @@ -115,7 +117,8 @@ command: mirna_quantification.py SAM --count --len --mir-list isomir output: hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTAA 4.333333333333333 6 23 hsa-miR-512-3p|0|1|23M|3T18C0|AAGGGCTGTCATAGCTGAGGTAA 12.0 8 19 -""" +""" # noqa: E501 +# pylint: enable=line-too-long import argparse from pathlib import Path @@ -285,7 +288,6 @@ def collapsed_contribution(aln: pysam.AlignedSegment) -> float: Alignment to which the overall contribution is calculated Returns: - Contribution of alignment to overall count """ name = str(aln.query_name) @@ -372,7 +374,8 @@ def get_name(pre_name: str) -> list[str]: Args: pre_name: - string with the format FEAT_NAME|5p-SHIFT|3p-SHIFT|CIGAR|MD|READ_SEQ + string with the format + FEAT_NAME|5p-SHIFT|3p-SHIFT|CIGAR|MD|READ_SEQ Returns: list with the species name to be found in the final table and its type