From 36bd39a654265e408589185b1f65ada7cb34679a Mon Sep 17 00:00:00 2001 From: Jover Date: Tue, 29 Aug 2023 12:00:19 -0700 Subject: [PATCH] config/clades: remove excess whitespace Discovered as part of https://github.com/nextstrain/augur/pull/1293 that the clade TSVs for this repo has excess whitespace which causes it to bypass the default `skip_blank_lines=True` behavior for `pandas.read_csv`. The issue has been fixed in Augur, but still nice to remove the excess whitespace here to keep things uniform with other pathogen clade TSVs. Note that the trailing whitespace after inherited clade definitions are required. --- config/clades_G_a.tsv | 42 ++++++++++++++++---------------- config/clades_G_b.tsv | 28 ++++++++++----------- config/clades_genome_a.tsv | 50 +++++++++++++++++++------------------- config/clades_genome_b.tsv | 10 ++++---- 4 files changed, 65 insertions(+), 65 deletions(-) diff --git a/config/clades_G_a.tsv b/config/clades_G_a.tsv index c157af9..69c5503 100644 --- a/config/clades_G_a.tsv +++ b/config/clades_G_a.tsv @@ -3,80 +3,80 @@ GA1 G 141 A GA1 G 121 G GA1 G 244 I GA1 G 296 P - + GA2 G 111 P - + GA2.1 G 229 N - + GA2.2 G 122 A GA2.2 G 114 T GA2.2 G 115 P - + GA2.3 G 122 A GA2.3 G 156 Q GA2.3 G 289 S GA2.3 G 269 T - + GA2.3.1 clade GA2.3 GA2.3.1 G 254 E GA2.3.1 G 252 I - + GA2.3.2 clade GA2.3 GA2.3.2 G 133 I - + GA2.3.2a clade GA2.3.2 GA2.3.2a G 242 S GA2.3.2a G 225 I - + GA2.3.2b clade GA2.3.2 GA2.3.2b G 112 I GA2.3.2b G 141 M GA2.3.2b G 244 K - + GA2.3.3 clade GA2.3 GA2.3.3 G 111 S GA2.3.3 G 292 S - + GA2.3.4 clade GA2.3 GA2.3.4 G 273 Y GA2.3.4 G 210 L - + GA2.3.5 clade GA2.3 GA2.3.5 G 232 G GA2.3.5 G 253 K - + GA3 G 111 T GA3 G 250 N - + GA3.0.0 G 111 T GA3.0.0 G 250 N - + GA3.0.1 G 102 F GA3.0.1 G 193 S GA3.0.1 G 295 I - + GA3.0.2 clade GA3 GA3.0.2 G 113 A GA3.0.2 G 125 I GA3.0.2 G 274 T - + GA3.0.3 clade GA3 GA3.0.3 G 161 D GA3.0.3 G 297 D - + GA3.0.3a clade GA3.0.3 GA3.0.3a G 232 D - + GA3.0.4a clade GA3.0.3a GA3.0.4a G 227 S - + GA3.0.3b clade GA3.0.3 - + GA3.0.4b clade GA3.0.3b GA3.0.4b G 219 P GA3.0.4b G 224 P GA3.0.4b G 208 Q GA3.0.4b G 246 L - + GA3.0.5b clade GA3.0.4b GA3.0.5b G 153 K diff --git a/config/clades_G_b.tsv b/config/clades_G_b.tsv index 6e634f6..8b6c53a 100644 --- a/config/clades_G_b.tsv +++ b/config/clades_G_b.tsv @@ -3,50 +3,50 @@ GB1 G 150 S GB1 G 280 I GB1 G 208 I GB1 G 222 M - + GB2 G 118 T GB2 G 223 T GB2 G 257 L - + GB3 G 136 I GB3 G 71 P GB3 G 109 L - + GB4 G 222 A GB4 G 219 S GB4 G 258 D - + GB5 G 143 N GB5 G 237 P - + GB5.0.0 G 143 N GB5.0.0 G 237 P - + GB5.0.1 clade GB5 GB5.0.1 G 247 P - + GB5.0.2 clade GB5.0.1 GB5.0.2 G 223 P GB5.0.2 G 138 S - + GB5.0.3 clade GB5.0.2 GB5.0.3 G 269 A - + GB5.0.4a G 282 T GB5.0.4a G 200 T - + GB5.0.5a clade GB5.0.0 GB5.0.5a G 136 T - + GB5.0.4b G 153 R GB5.0.4b G 266 L - + GB5.0.4c clade GB5.0.3 GB5.0.4c G 285 D - + GB7 G 242 K GB7 G 214 I - + GB6 G 235 L GB6 G 126 K GB6 G 262 P diff --git a/config/clades_genome_a.tsv b/config/clades_genome_a.tsv index 1e2ecf1..732301c 100644 --- a/config/clades_genome_a.tsv +++ b/config/clades_genome_a.tsv @@ -5,91 +5,91 @@ A1 nuc 479 T A1 nuc 861 G A1 F 16 I A1 L 81 L - + A2 clade A1 A2 G 110 L A2 G 197 R A2 L 2016 I - + A3 nuc 3026 A A3 nuc 4019 A A3 nuc 4416 A - + A4 nuc 7516 G A4 nuc 13658 G - + A5 nuc 4905 G A5 nuc 5588 G A5 nuc 7501 C A5 nuc 8577 C A5 nuc 11541 C - + A6 nuc 134 C A6 nuc 1281 G - + A7 nuc 3070 G A7 nuc 3998 T A7 nuc 4013 C A7 nuc 3536 C - + A8 nuc 603 T A8 nuc 1949 A A8 nuc 2516 C A8 nuc 3155 T - + A9 clade A8 A9 nuc 3188 G A9 nuc 5113 G A9 nuc 4220 C - + A10 clade A9 A10 nuc 2541 A A10 nuc 3188 A A10 G 117 S A10 nuc 4982 C - - + + A11 nuc 5642 G A11 nuc 7369 T A11 nuc 9213 T - - + + A12 nuc 2934 C A12 nuc 7919 A A12 nuc 10506 T A12 nuc 13251 G - + A13 nuc 89 G A13 N 84 K - + A14 nuc 1349 T A14 nuc 3994 A A14 nuc 5619 T - + A15 nuc 46 A A15 nuc 4226 G - + A16 nuc 6064 C A16 nuc 9379 T - - + + A17 L 216 S A17 F 574 S - + A18 G 297 K A18 L 217 P - + A19 clade A18 A19 G 133 I - + A20 nuc 8976 C - + A21 nuc 461 C - + A22 nuc 47 C A22 nuc 1910 G A22 nuc 4467 C - + A23 clade A20 A23 nuc 1223 T A23 nuc 2066 G diff --git a/config/clades_genome_b.tsv b/config/clades_genome_b.tsv index cdb0601..5d02851 100644 --- a/config/clades_genome_b.tsv +++ b/config/clades_genome_b.tsv @@ -1,19 +1,19 @@ clade gene site alt B1 L 232 T B1 G 261 T - + B2 G 154 I B2 G 77 S - + B3 G 152 L B3 nuc 381 C - + B5 G 255 A B5 G 258 G - + B4 nuc 1235 A B4 G 116 T - + B6 nuc 1082 G B6 nuc 3325 C B6 nuc 3634 A