From c2178abb800fb70e4eb1a80c89a27a1c6595f1d1 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 9 Feb 2024 16:58:15 +0100
Subject: [PATCH] Update getPanachePAV.sh
Fixed bug in awk command used to rename columns in final PAV matrix
---
scripts/getPanachePAV.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/getPanachePAV.sh b/scripts/getPanachePAV.sh
index 719b4cf..f518966 100644
--- a/scripts/getPanachePAV.sh
+++ b/scripts/getPanachePAV.sh
@@ -42,7 +42,7 @@ awk -F'\t' 'BEGIN {OFS="\t"} NR==1 {print $1, $2, $3, $4, "temp", "temp", $5, $6
mv ${chrdir}/temp1.tsv ${chrdir}/$chrname.untangle.multiref.pavs.matrix.tsv
# Renaming columns for Panache
-awk -F'\t' 'BEGIN {FS=OFS="\t"} NR==1 {sub(${gfa}, "#Chromosome"); sub(${chrdir}, "FeatureStart"); sub(${output}, "FeatureStop"); sub(${appdir}, "Sequence_IUPAC_Plus"); sub($5, "SimilarBlocks"); sub($6, "Function")} {print}' \
+awk -F'\t' 'BEGIN {FS=OFS="\t"} NR==1 {sub($1, "#Chromosome"); sub($2, "FeatureStart"); sub($3, "FeatureStop"); sub($4, "Sequence_IUPAC_Plus"); sub($5, "SimilarBlocks"); sub($6, "Function")} {print}' \
${chrdir}/$chrname.untangle.multiref.pavs.matrix.tsv > ${chrdir}/temp2.tsv && \
mv ${chrdir}/temp2.tsv ${chrdir}/$chrname.untangle.multiref.pavs.matrix.tsv
--
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