Use standard line endings for index output

Sets standard UNIX-style line endings for sequence index outputs, for consistency across Augur outputs.
nextstrain · Apr 22, 2022 · 0e164de · 0e164de
1 parent ec76046
commit 0e164de
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/augur/index.py b/augur/index.py
@@ -177,7 +177,7 @@ def index_sequences(sequences_path, sequence_index_path):
     num_of_seqs = 0
 
     with open_file(sequence_index_path, 'wt') as out_file:
-        tsv_writer = csv.writer(out_file, delimiter = '\t')
+        tsv_writer = csv.writer(out_file, delimiter = '\t', lineterminator='\n')
 
         #write header i output file
         header = ['strain', 'length']+labels+['invalid_nucleotides']

diff --git a/tests/builds/zika/results/sequence_index.tsv b/tests/builds/zika/results/sequence_index.tsv
@@ -1,13 +1,13 @@
-strain	length	A	C	G	T	N	other_IUPAC	-	?	invalid_nucleotides
-PAN/CDC_259359_V1_V3/2015	10771	2952	2379	3142	2298	0	0	0	0	0
-COL/FLR_00024/2015	10659	2921	2344	3113	2281	0	0	0	0	0
-PRVABC59	10675	2923	2351	3115	2286	0	0	0	0	0
-COL/FLR_00008/2015	10659	2924	2344	3110	2281	0	0	0	0	0
-Colombia/2016/ZC204Se	10608	2907	2332	3093	2275	0	1	0	0	0
-ZKC2/2016	10807	2955	2389	3159	2304	0	0	0	0	0
-VEN/UF_1/2016	10808	2958	2383	3152	2315	0	0	0	0	0
-DOM/2016/BB_0059	10035	2563	2089	2741	2015	621	6	0	0	0
-BRA/2016/FC_6706	10366	2747	2203	2915	2165	329	7	0	0	0
-DOM/2016/BB_0183	10621	2910	2343	3099	2269	0	0	0	0	0
-EcEs062_16	10812	2960	2388	3158	2306	0	0	0	0	0
-HND/2016/HU_ME59	10365	2842	2271	3016	2233	0	3	0	0	0
+strain	length	A	C	G	T	N	other_IUPAC	-	?	invalid_nucleotides
+PAN/CDC_259359_V1_V3/2015	10771	2952	2379	3142	2298	0	0	0	0	0
+COL/FLR_00024/2015	10659	2921	2344	3113	2281	0	0	0	0	0
+PRVABC59	10675	2923	2351	3115	2286	0	0	0	0	0
+COL/FLR_00008/2015	10659	2924	2344	3110	2281	0	0	0	0	0
+Colombia/2016/ZC204Se	10608	2907	2332	3093	2275	0	1	0	0	0
+ZKC2/2016	10807	2955	2389	3159	2304	0	0	0	0	0
+VEN/UF_1/2016	10808	2958	2383	3152	2315	0	0	0	0	0
+DOM/2016/BB_0059	10035	2563	2089	2741	2015	621	6	0	0	0
+BRA/2016/FC_6706	10366	2747	2203	2915	2165	329	7	0	0	0
+DOM/2016/BB_0183	10621	2910	2343	3099	2269	0	0	0	0	0
+EcEs062_16	10812	2960	2388	3158	2306	0	0	0	0	0
+HND/2016/HU_ME59	10365	2842	2271	3016	2233	0	3	0	0	0
diff --git a/tests/builds/zika/results/sequence_index.tsv.gz b/tests/builds/zika/results/sequence_index.tsv.gz