From 3a643ccaaf3bfe912d2aa5e4354fde472a59c95c Mon Sep 17 00:00:00 2001 From: "lucia.pena.perez@scilifelab.se" Date: Mon, 14 Aug 2023 18:09:46 +0200 Subject: [PATCH] fix further clarify --- bin/drop_sample_annot.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/drop_sample_annot.py b/bin/drop_sample_annot.py index 4b490bdd..d2d62731 100755 --- a/bin/drop_sample_annot.py +++ b/bin/drop_sample_annot.py @@ -53,7 +53,7 @@ def __init__(self, bam, sample, strandedness, single_end, gtf, count_file, out_f def final_annot(count_file: Path, ref_annot: Path, out_file: Path): """Concatinates the Sample Annotation produced by SampleAnnotation with the one provided for the reference samples, checking for duplicate sample IDs""" - df_samples = pd.read_csv("drop_pt_annot.tsv", sep="\t") + df_samples = pd.read_csv("drop_annotation_given_samples.tsv", sep="\t") df_reference = pd.read_csv(ref_annot, sep="\t") df_reference["GENE_COUNTS_FILE"] = count_file df_samples["COUNT_OVERLAPS"] = df_reference["COUNT_OVERLAPS"].iloc[0] @@ -131,6 +131,6 @@ def final_annot(count_file: Path, ref_annot: Path, out_file: Path): args = parser.parse_args() SampleAnnotation( - args.bam, args.sample, args.strandedness, args.single_end, args.gtf, args.count_file, "drop_pt_annot.tsv" + args.bam, args.sample, args.strandedness, args.single_end, args.gtf, args.count_file, "drop_annotation_given_samples.tsv" ) final_annot(args.count_file, args.ref_annot, args.output)