From 915672e9db021588349ede4e23f21003455eb705 Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Wed, 26 Jun 2024 16:47:19 -0700
Subject: [PATCH] write_records_to_tsv: Stop quoting output TSV
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According to TSV specs,¹ there are no restrictions on special characters
other than tabs are not allowed in a field. This is different from the
CSV specs,² which require double quotes around fields that contain
special characters.

Since this function only produces TSVs, follow the TSV specs and stop
adding quotes.

Resolves <https://github.com/nextstrain/augur/issues/1312>

¹ <https://www.iana.org/assignments/media-types/text/tab-separated-values>
² <https://datatracker.ietf.org/doc/html/rfc4180#page-2>
---
 augur/io/metadata.py      | 4 +++-
 tests/io/test_metadata.py | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/augur/io/metadata.py b/augur/io/metadata.py
index 32747eceb..bcaef5b79 100644
--- a/augur/io/metadata.py
+++ b/augur/io/metadata.py
@@ -483,7 +483,9 @@ def write_records_to_tsv(records, output_file):
             output_columns,
             extrasaction='ignore',
             delimiter='\t',
-            lineterminator='\n'
+            lineterminator='\n',
+            quoting=csv.QUOTE_NONE,
+            quotechar=None,
         )
         tsv_writer.writeheader()
         tsv_writer.writerow(first_record)
diff --git a/tests/io/test_metadata.py b/tests/io/test_metadata.py
index 301e841e2..45ec13f10 100644
--- a/tests/io/test_metadata.py
+++ b/tests/io/test_metadata.py
@@ -466,7 +466,7 @@ def output_records():
 def expected_output_tsv():
     return (
         "strain\tcountry\tdate\n"
-        'SEQ_A\t"""USA"""\t2020-10-01\n'
+        'SEQ_A\t"USA"\t2020-10-01\n'
         "SEQ_T\tUSA\t2020-10-02\n"
     )