From fdb401bff26e7b588adbe6e221b969d247750e2f Mon Sep 17 00:00:00 2001 From: Alex Thomas Date: Tue, 14 Nov 2023 12:57:19 +0000 Subject: [PATCH] fmt --- workflow/scripts/masking.py | 2 -- workflow/scripts/quality-filter.py | 4 +--- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/workflow/scripts/masking.py b/workflow/scripts/masking.py index c5a3b6e1..1e2e74a2 100644 --- a/workflow/scripts/masking.py +++ b/workflow/scripts/masking.py @@ -48,7 +48,6 @@ def get_base_count(pileupcolumn): for pileupread in pileupcolumn.pileups: # TODO Check pileupread for missing bases if not pileupread.is_del and not pileupread.is_refskip: - read_base = pileupread.alignment.query_sequence[pileupread.query_position] bases.append(read_base) @@ -102,7 +101,6 @@ def mask_sequence(sequence, coverages, base_counts): covered_postions = coverages.keys() for position, base in enumerate(sequence): - if position not in covered_postions: # TODO Check why there are postions that are not covered by any reads and are not Ns # sequence[position] = "N" diff --git a/workflow/scripts/quality-filter.py b/workflow/scripts/quality-filter.py index eb0a5abe..68977de2 100644 --- a/workflow/scripts/quality-filter.py +++ b/workflow/scripts/quality-filter.py @@ -31,9 +31,7 @@ def get_identity(quast_report_paths: List[str]) -> dict: sample = path.dirname(report_path).split("/")[-1] # load report - report_df = pd.read_csv( - report_path, delimiter="\t", names=["name", "value"] - ) + report_df = pd.read_csv(report_path, delimiter="\t", names=["name", "value"]) report_df.set_index("name", inplace=True) # select genome fraction (%) try: