From c355cfa86a126d36b114db6ffe041d0239fa69fb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 25 May 2021 14:23:47 +0200
Subject: [PATCH] gffread: add awk cmd to remove duplicated transcript
---
src/nf_modules/gffread/main.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
index dcc4bf5e..07e010e7 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -25,6 +25,7 @@ process gffread {
file_prefix = file_id
}
"""
- gffread ${gtf} -g ${fasta} -M -x ${file_prefix}.fasta
+ gffread ${gtf} -g ${fasta} -M -x dup_${file_prefix}.fasta
+ awk 'BEGIN {i = 1;} { if (\$1 ~ /^>/) { tmp = h[i]; h[i] = \$1; } else if (!a[\$1]) { s[i] = \$1; a[\$1] = "1"; i++; } else { h[i] = tmp; } } END { for (j = 1; j < i; j++) { print h[j]; print s[j]; } }' < dup_${file_prefix}.fasta > ${file_prefix}.fasta
"""
}
--
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