From cc557a64bb489bb39c3abf932a6cdfb87ad4a383 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 20 Apr 2020 17:25:37 -0400
Subject: Make sure there is a newline in relabeled fasta (but no blank lines)

---
 workflows/pangenome-generate/relabel-seqs.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'workflows/pangenome-generate')

diff --git a/workflows/pangenome-generate/relabel-seqs.py b/workflows/pangenome-generate/relabel-seqs.py
index b558fe2..1188ceb 100644
--- a/workflows/pangenome-generate/relabel-seqs.py
+++ b/workflows/pangenome-generate/relabel-seqs.py
@@ -12,4 +12,7 @@ for i, r in enumerate(reads):
         data = fa.read(8096)
         while data:
             relabeled_fasta.write(data)
+            endswithnewline = data.endswith("\\n")
             data = fa.read(8096)
+        if not endswithnewline:
+            relabeled_fasta.write("\\n")
-- 
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