From 56ff76d50bc3f411bcaf8b9259f88a8c78c3fb2d Mon Sep 17 00:00:00 2001 From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com> Date: Thu, 2 May 2024 10:45:24 +0200 Subject: [PATCH] typo --- .../workflow/scripts/performance_measures_snvs_freqs.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/scripts/performance_measures_snvs_freqs.py b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/scripts/performance_measures_snvs_freqs.py index 5e02667f..d9d0e6db 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/scripts/performance_measures_snvs_freqs.py +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/scripts/performance_measures_snvs_freqs.py @@ -26,7 +26,6 @@ def convert_vcf(fname): zero_based_pos = variant.POS - 1 # VCF is 1-based variant_list.add(f"{zero_based_pos}{base}") return variant_list -vim def convert_groundtruth(fname): df = pd.read_csv(fname, index_col=0) @@ -49,7 +48,7 @@ def mutation_calls_details(vcf_list, groundtruth_list): for iter_row, gt_row in pd.read_csv(fname_groundtruth, index_col=0).iterrows(): true_variant = str(gt_row["position"]) + gt_row["variant"] mutation_type = str(gt_row["type"]) - if method.startswith(('lofreq', 'shorah'): + if method.startswith(('lofreq', 'shorah')): is_false_negative = True for variant in VCF(fname_vcf): for idx_base, base in enumerate(variant.ALT):