From c120767321fb50ff5cbc25398a2d86dbf40f673a Mon Sep 17 00:00:00 2001 From: Karan Jaisingh Date: Fri, 8 Nov 2024 20:59:57 -0500 Subject: [PATCH] Modify EvidenceQC to not create/expect additional column in median coverage file (#745) * Modified python scripts to not create/expect additional column * Removed iloc call --- src/WGD/bin/medianCoverage.R | 2 +- src/sv-pipeline/scripts/make_evidence_qc_table.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/WGD/bin/medianCoverage.R b/src/WGD/bin/medianCoverage.R index 8db8738a6..319704008 100755 --- a/src/WGD/bin/medianCoverage.R +++ b/src/WGD/bin/medianCoverage.R @@ -122,6 +122,6 @@ if(opts$binwise==TRUE){ write.table(res,args$args[2], sep="\t", col.names=T, row.names=F, quote=F) }else{ res <- covPerSample(cov,mad=opts$mad) - names(res)[1] <- "sample_id" + names(res)[1] <- "#sample_id" write.table(res,args$args[2], sep="\t", col.names=T, row.names=F, quote=F) } diff --git a/src/sv-pipeline/scripts/make_evidence_qc_table.py b/src/sv-pipeline/scripts/make_evidence_qc_table.py index 87d9e89d1..2005664bf 100644 --- a/src/sv-pipeline/scripts/make_evidence_qc_table.py +++ b/src/sv-pipeline/scripts/make_evidence_qc_table.py @@ -51,7 +51,7 @@ def read_bincov_median(filename: str) -> pd.DataFrame: df_median = pd.read_csv(filename, sep="\t").T df_median = df_median.rename_axis(ID_COL).reset_index() df_median.columns = [ID_COL, "median_coverage"] - df_median = df_median.iloc[1:].reset_index(drop=True) + df_median = df_median.reset_index(drop=True) return df_median