From 1262643b53ed7f163f8017407fd0d6f777a5b946 Mon Sep 17 00:00:00 2001 From: Thomas Roder Date: Tue, 28 Jul 2020 14:07:05 +0200 Subject: [PATCH] added chances made by ViriatoII (github.com/davidemms/OrthoFinder/pull/434) - compatible with new N0.tsv structure - small tweek to ignore proteins annotated AbInitio with maker, which don't have useful information, and to be resilient to gene names missing in the corresponding fastas --- data/Orthogroups.tsv | 10230 +++++++++++++--------- data/SpeciesTree_rooted.txt | 2 +- data/SpeciesTree_rooted_node_labels.txt | 2 +- orthogroup_to_gene_name.py | 34 +- 4 files changed, 6052 insertions(+), 4216 deletions(-) diff --git a/data/Orthogroups.tsv b/data/Orthogroups.tsv index 7bb7a8f..88d53a8 100644 --- a/data/Orthogroups.tsv +++ b/data/Orthogroups.tsv @@ -1,4205 +1,6025 @@ -Orthogroup FAM10859 FAM18099 FAM18101 FAM18105 FAM18108 FAM18110 FAM18113 FAM18119 FAM18121 FAM18123 FAM18124 FAM18126 FAM18129 FAM18132 FAM18149 FAM18157 FAM18168 FAM18172 FAM18175 FAM19353 FAM19404 FAM22276 FAM22277 FAM22278 FAM22279 FAM22280 FAM22436 FAM22437 FAM23964 FAM23965 FAM23966 FAM23967 FAM3228 FAM3248 FAM3257 FAM4067 FAM6012 FAM6161 FAM6165 FAM6410 FAM7821 FAM8140 FAM8374 FAM8407 -OG0000000 gnl|extdb|FAM10859_000352, gnl|extdb|FAM10859_000356, gnl|extdb|FAM10859_000362, gnl|extdb|FAM10859_000368, gnl|extdb|FAM10859_000709, gnl|extdb|FAM10859_000716, gnl|extdb|FAM10859_003169 gnl|extdb|FAM18099_000096, gnl|extdb|FAM18099_000440, gnl|extdb|FAM18099_000846, gnl|extdb|FAM18099_001766, gnl|extdb|FAM18099_001799, gnl|extdb|FAM18099_002200, gnl|extdb|FAM18099_002697, gnl|extdb|FAM18099_002794, gnl|extdb|FAM18099_002994, gnl|extdb|FAM18099_003018, gnl|extdb|FAM18099_003036, gnl|extdb|FAM18099_003063 gnl|extdb|FAM18101_000123, gnl|extdb|FAM18101_000130, gnl|extdb|FAM18101_000152, gnl|extdb|FAM18101_000670, gnl|extdb|FAM18101_000697, gnl|extdb|FAM18101_000707, gnl|extdb|FAM18101_000722, gnl|extdb|FAM18101_000727, gnl|extdb|FAM18101_000739, gnl|extdb|FAM18101_001306, gnl|extdb|FAM18101_001464, gnl|extdb|FAM18101_002854, gnl|extdb|FAM18101_002887 gnl|extdb|FAM18105_000104, gnl|extdb|FAM18105_000109, gnl|extdb|FAM18105_000610, gnl|extdb|FAM18105_000627, gnl|extdb|FAM18105_000638, gnl|extdb|FAM18105_000652, gnl|extdb|FAM18105_000662, gnl|extdb|FAM18105_000672, gnl|extdb|FAM18105_001293, gnl|extdb|FAM18105_001330, gnl|extdb|FAM18105_002526, gnl|extdb|FAM18105_002703, gnl|extdb|FAM18105_002724 gnl|extdb|FAM18108_000797, gnl|extdb|FAM18108_000804, gnl|extdb|FAM18108_002177, gnl|extdb|FAM18108_003123, gnl|extdb|FAM18108_003146, gnl|extdb|FAM18108_003175, gnl|extdb|FAM18108_003247 gnl|extdb|FAM18110_000155, gnl|extdb|FAM18110_000183, gnl|extdb|FAM18110_000547, gnl|extdb|FAM18110_000552, gnl|extdb|FAM18110_000684, gnl|extdb|FAM18110_000685, gnl|extdb|FAM18110_002014, gnl|extdb|FAM18110_002029, gnl|extdb|FAM18110_002983, gnl|extdb|FAM18110_003141, gnl|extdb|FAM18110_003189, gnl|extdb|FAM18110_003197, gnl|extdb|FAM18110_003211, gnl|extdb|FAM18110_003228, gnl|extdb|FAM18110_003229, gnl|extdb|FAM18110_003263 gnl|extdb|FAM18113_000024, gnl|extdb|FAM18113_000131, gnl|extdb|FAM18113_000144, gnl|extdb|FAM18113_000156, gnl|extdb|FAM18113_000162, gnl|extdb|FAM18113_002907, gnl|extdb|FAM18113_002926, gnl|extdb|FAM18113_002927 gnl|extdb|FAM18119_000078, gnl|extdb|FAM18119_000627, gnl|extdb|FAM18119_001429, gnl|extdb|FAM18119_002033, gnl|extdb|FAM18119_002830, gnl|extdb|FAM18119_003030, gnl|extdb|FAM18119_003039, gnl|extdb|FAM18119_003083, gnl|extdb|FAM18119_003111, gnl|extdb|FAM18119_003138 gnl|extdb|FAM18121_000098, gnl|extdb|FAM18121_000103, gnl|extdb|FAM18121_000132, gnl|extdb|FAM18121_000334, gnl|extdb|FAM18121_000344, gnl|extdb|FAM18121_000409, gnl|extdb|FAM18121_000486, gnl|extdb|FAM18121_002957, gnl|extdb|FAM18121_003040, gnl|extdb|FAM18121_003052 gnl|extdb|FAM18123_000280, gnl|extdb|FAM18123_000757, gnl|extdb|FAM18123_000765, gnl|extdb|FAM18123_002043, gnl|extdb|FAM18123_002056, gnl|extdb|FAM18123_002073, gnl|extdb|FAM18123_002890, gnl|extdb|FAM18123_003026, gnl|extdb|FAM18123_003099, gnl|extdb|FAM18123_003147, gnl|extdb|FAM18123_003196, gnl|extdb|FAM18123_003242, gnl|extdb|FAM18123_003342 gnl|extdb|FAM18124_000004, gnl|extdb|FAM18124_000142, gnl|extdb|FAM18124_000457, gnl|extdb|FAM18124_000463, gnl|extdb|FAM18124_000470, gnl|extdb|FAM18124_000498, gnl|extdb|FAM18124_000506, gnl|extdb|FAM18124_000634, gnl|extdb|FAM18124_001288, gnl|extdb|FAM18124_002657, gnl|extdb|FAM18124_002810, gnl|extdb|FAM18124_003047, gnl|extdb|FAM18124_003051 gnl|extdb|FAM18126_000161, gnl|extdb|FAM18126_000410, gnl|extdb|FAM18126_000644, gnl|extdb|FAM18126_000655, gnl|extdb|FAM18126_000671, gnl|extdb|FAM18126_000672, gnl|extdb|FAM18126_000705, gnl|extdb|FAM18126_001367, gnl|extdb|FAM18126_001400, gnl|extdb|FAM18126_002590, gnl|extdb|FAM18126_003046, gnl|extdb|FAM18126_003075, gnl|extdb|FAM18126_003091, gnl|extdb|FAM18126_003247, gnl|extdb|FAM18126_003263, gnl|extdb|FAM18126_003273, gnl|extdb|FAM18126_003288, gnl|extdb|FAM18126_003293, gnl|extdb|FAM18126_003339, gnl|extdb|FAM18126_003341, gnl|extdb|FAM18126_003365, gnl|extdb|FAM18126_003382, gnl|extdb|FAM18126_003390, gnl|extdb|FAM18126_003391, gnl|extdb|FAM18126_003423 gnl|extdb|FAM18129_000199, gnl|extdb|FAM18129_000500, gnl|extdb|FAM18129_000538, gnl|extdb|FAM18129_000551, gnl|extdb|FAM18129_000714, gnl|extdb|FAM18129_001375, gnl|extdb|FAM18129_002916, gnl|extdb|FAM18129_003005, gnl|extdb|FAM18129_003059, gnl|extdb|FAM18129_003067 gnl|extdb|FAM18132_000116, gnl|extdb|FAM18132_000121, gnl|extdb|FAM18132_000137, gnl|extdb|FAM18132_000613, gnl|extdb|FAM18132_000624, gnl|extdb|FAM18132_000647, gnl|extdb|FAM18132_002594, gnl|extdb|FAM18132_002719, gnl|extdb|FAM18132_002747, gnl|extdb|FAM18132_002776 gnl|extdb|FAM18149_000008, gnl|extdb|FAM18149_000030, gnl|extdb|FAM18149_000162, gnl|extdb|FAM18149_000170, gnl|extdb|FAM18149_000243, gnl|extdb|FAM18149_000279, gnl|extdb|FAM18149_000324, gnl|extdb|FAM18149_001123, gnl|extdb|FAM18149_001134, gnl|extdb|FAM18149_001799, gnl|extdb|FAM18149_003025, gnl|extdb|FAM18149_003131, gnl|extdb|FAM18149_003146, gnl|extdb|FAM18149_003150, gnl|extdb|FAM18149_003187 gnl|extdb|FAM18157_000095, gnl|extdb|FAM18157_000096, gnl|extdb|FAM18157_000967, gnl|extdb|FAM18157_003008, gnl|extdb|FAM18157_003016, gnl|extdb|FAM18157_003046 gnl|extdb|FAM18168_000005, gnl|extdb|FAM18168_000006, gnl|extdb|FAM18168_000035, gnl|extdb|FAM18168_000123, gnl|extdb|FAM18168_000131, gnl|extdb|FAM18168_000132, gnl|extdb|FAM18168_000227, gnl|extdb|FAM18168_001057, gnl|extdb|FAM18168_001068, gnl|extdb|FAM18168_002205, gnl|extdb|FAM18168_002879, gnl|extdb|FAM18168_002918, gnl|extdb|FAM18168_003017, gnl|extdb|FAM18168_003027, gnl|extdb|FAM18168_003031, gnl|extdb|FAM18168_003042, gnl|extdb|FAM18168_003057, gnl|extdb|FAM18168_003060 gnl|extdb|FAM18172_000642, gnl|extdb|FAM18172_000645, gnl|extdb|FAM18172_000653, gnl|extdb|FAM18172_002110, gnl|extdb|FAM18172_002113, gnl|extdb|FAM18172_002891, gnl|extdb|FAM18172_003018, gnl|extdb|FAM18172_003144, gnl|extdb|FAM18172_003160, gnl|extdb|FAM18172_003168, gnl|extdb|FAM18172_003177, gnl|extdb|FAM18172_003241, gnl|extdb|FAM18172_003297, gnl|extdb|FAM18172_003298, gnl|extdb|FAM18172_003335 gnl|extdb|FAM18175_001384, gnl|extdb|FAM18175_001963, gnl|extdb|FAM18175_002139, gnl|extdb|FAM18175_003035, gnl|extdb|FAM18175_003100, gnl|extdb|FAM18175_003115, gnl|extdb|FAM18175_003134, gnl|extdb|FAM18175_003148, gnl|extdb|FAM18175_003151, gnl|extdb|FAM18175_003169 gnl|extdb|FAM19353_000226, gnl|extdb|FAM19353_000231, gnl|extdb|FAM19353_000238, gnl|extdb|FAM19353_000239, gnl|extdb|FAM19353_000271, gnl|extdb|FAM19353_000273 gnl|extdb|FAM19404_000014, gnl|extdb|FAM19404_000022, gnl|extdb|FAM19404_000491, gnl|extdb|FAM19404_000580, gnl|extdb|FAM19404_000691, gnl|extdb|FAM19404_001810, gnl|extdb|FAM19404_001831 gnl|extdb|FAM22276_000307, gnl|extdb|FAM22276_000558, gnl|extdb|FAM22276_000566, gnl|extdb|FAM22276_000569, gnl|extdb|FAM22276_000576, gnl|extdb|FAM22276_001707, gnl|extdb|FAM22276_001708, gnl|extdb|FAM22276_002973, gnl|extdb|FAM22276_002977 gnl|extdb|FAM22277_000503, gnl|extdb|FAM22277_000513, gnl|extdb|FAM22277_001896, gnl|extdb|FAM22277_002329, gnl|extdb|FAM22277_002992, gnl|extdb|FAM22277_003004, gnl|extdb|FAM22277_003051 gnl|extdb|FAM22278_000005, gnl|extdb|FAM22278_000024, gnl|extdb|FAM22278_000164, gnl|extdb|FAM22278_001019, gnl|extdb|FAM22278_002001, gnl|extdb|FAM22278_002740, gnl|extdb|FAM22278_002878, gnl|extdb|FAM22278_002936, gnl|extdb|FAM22278_002940, gnl|extdb|FAM22278_002947, gnl|extdb|FAM22278_002964, gnl|extdb|FAM22278_002998, gnl|extdb|FAM22278_003001, gnl|extdb|FAM22278_003051, gnl|extdb|FAM22278_003053, gnl|extdb|FAM22278_003098, gnl|extdb|FAM22278_003126 gnl|extdb|FAM22279_000246, gnl|extdb|FAM22279_000252, gnl|extdb|FAM22279_000382, gnl|extdb|FAM22279_000821, gnl|extdb|FAM22279_001390, gnl|extdb|FAM22279_001717, gnl|extdb|FAM22279_001830, gnl|extdb|FAM22279_002295, gnl|extdb|FAM22279_003037, gnl|extdb|FAM22279_003048, gnl|extdb|FAM22279_003099, gnl|extdb|FAM22279_003158 gnl|extdb|FAM22280_000143, gnl|extdb|FAM22280_000151, gnl|extdb|FAM22280_000224, gnl|extdb|FAM22280_000243, gnl|extdb|FAM22280_001326, gnl|extdb|FAM22280_001553, gnl|extdb|FAM22280_002873, gnl|extdb|FAM22280_002906, gnl|extdb|FAM22280_002911, gnl|extdb|FAM22280_002919, gnl|extdb|FAM22280_002926, gnl|extdb|FAM22280_003009, gnl|extdb|FAM22280_003028, gnl|extdb|FAM22280_003049, gnl|extdb|FAM22280_003052, gnl|extdb|FAM22280_003057, gnl|extdb|FAM22280_003082, gnl|extdb|FAM22280_003107, gnl|extdb|FAM22280_003140, gnl|extdb|FAM22280_003143, gnl|extdb|FAM22280_003151, gnl|extdb|FAM22280_003155 gnl|extdb|FAM22436_002045, gnl|extdb|FAM22436_002052, gnl|extdb|FAM22436_002273, gnl|extdb|FAM22436_002546, gnl|extdb|FAM22436_002561, gnl|extdb|FAM22436_002604, gnl|extdb|FAM22436_002831, gnl|extdb|FAM22436_002839, gnl|extdb|FAM22436_002917, gnl|extdb|FAM22436_002927, gnl|extdb|FAM22436_002946, gnl|extdb|FAM22436_002968, gnl|extdb|FAM22436_002975, gnl|extdb|FAM22436_003015, gnl|extdb|FAM22436_003092, gnl|extdb|FAM22436_003197, gnl|extdb|FAM22436_003201, gnl|extdb|FAM22436_003205 gnl|extdb|FAM22437_002040, gnl|extdb|FAM22437_002256, gnl|extdb|FAM22437_002715, gnl|extdb|FAM22437_002726, gnl|extdb|FAM22437_002832, gnl|extdb|FAM22437_002840, gnl|extdb|FAM22437_002856, gnl|extdb|FAM22437_002891, gnl|extdb|FAM22437_002911, gnl|extdb|FAM22437_002924, gnl|extdb|FAM22437_002934, gnl|extdb|FAM22437_002953, gnl|extdb|FAM22437_002960, gnl|extdb|FAM22437_002984, gnl|extdb|FAM22437_003015, gnl|extdb|FAM22437_003104, gnl|extdb|FAM22437_003136 gnl|extdb|FAM23964_001121, gnl|extdb|FAM23964_002004, gnl|extdb|FAM23964_002413, gnl|extdb|FAM23964_002512, gnl|extdb|FAM23964_002688, gnl|extdb|FAM23964_002708, gnl|extdb|FAM23964_002752, gnl|extdb|FAM23964_002793, gnl|extdb|FAM23964_002817, gnl|extdb|FAM23964_002831, gnl|extdb|FAM23964_002837, gnl|extdb|FAM23964_002843, gnl|extdb|FAM23964_002856, gnl|extdb|FAM23964_002862, gnl|extdb|FAM23964_002879, gnl|extdb|FAM23964_002894, gnl|extdb|FAM23964_002997, gnl|extdb|FAM23964_003024, gnl|extdb|FAM23964_003049, gnl|extdb|FAM23964_003094, gnl|extdb|FAM23964_003110, gnl|extdb|FAM23964_003127, gnl|extdb|FAM23964_003142, gnl|extdb|FAM23964_003143, gnl|extdb|FAM23964_003147 gnl|extdb|FAM23965_001085, gnl|extdb|FAM23965_001140, gnl|extdb|FAM23965_001268, gnl|extdb|FAM23965_002037, gnl|extdb|FAM23965_002604, gnl|extdb|FAM23965_002736, gnl|extdb|FAM23965_002744, gnl|extdb|FAM23965_002830, gnl|extdb|FAM23965_002840, gnl|extdb|FAM23965_002856, gnl|extdb|FAM23965_002884, gnl|extdb|FAM23965_002974, gnl|extdb|FAM23965_002990, gnl|extdb|FAM23965_002994 gnl|extdb|FAM23966_002805, gnl|extdb|FAM23966_002893, gnl|extdb|FAM23966_002901, gnl|extdb|FAM23966_002907, gnl|extdb|FAM23966_003020, gnl|extdb|FAM23966_003190, gnl|extdb|FAM23966_003198, gnl|extdb|FAM23966_003207, gnl|extdb|FAM23966_003220, gnl|extdb|FAM23966_003280 gnl|extdb|FAM23967_002807, gnl|extdb|FAM23967_002987, gnl|extdb|FAM23967_003164, gnl|extdb|FAM23967_003193, gnl|extdb|FAM23967_003212, gnl|extdb|FAM23967_003213, gnl|extdb|FAM23967_003221 gnl|extdb|FAM3228_000332, gnl|extdb|FAM3228_000337, gnl|extdb|FAM3228_000344, gnl|extdb|FAM3228_000394, gnl|extdb|FAM3228_000396, gnl|extdb|FAM3228_000410 gnl|extdb|FAM3248_000214, gnl|extdb|FAM3248_000574, gnl|extdb|FAM3248_000582, gnl|extdb|FAM3248_000587, gnl|extdb|FAM3248_000594, gnl|extdb|FAM3248_001682, gnl|extdb|FAM3248_001684, gnl|extdb|FAM3248_002964, gnl|extdb|FAM3248_002971 gnl|extdb|FAM3257_000001, gnl|extdb|FAM3257_000073, gnl|extdb|FAM3257_000405, gnl|extdb|FAM3257_000409, gnl|extdb|FAM3257_000458, gnl|extdb|FAM3257_001960, gnl|extdb|FAM3257_003319, gnl|extdb|FAM3257_003346 gnl|extdb|FAM4067_000297, gnl|extdb|FAM4067_000664, gnl|extdb|FAM4067_000670, gnl|extdb|FAM4067_000672, gnl|extdb|FAM4067_000817, gnl|extdb|FAM4067_001252, gnl|extdb|FAM4067_003141, gnl|extdb|FAM4067_003187 gnl|extdb|FAM6012_000005, gnl|extdb|FAM6012_000023, gnl|extdb|FAM6012_000145, gnl|extdb|FAM6012_000153, gnl|extdb|FAM6012_000154, gnl|extdb|FAM6012_000170, gnl|extdb|FAM6012_000264, gnl|extdb|FAM6012_000277, gnl|extdb|FAM6012_000350, gnl|extdb|FAM6012_001637, gnl|extdb|FAM6012_002684, gnl|extdb|FAM6012_002840, gnl|extdb|FAM6012_002981, gnl|extdb|FAM6012_003062, gnl|extdb|FAM6012_003067, gnl|extdb|FAM6012_003074, gnl|extdb|FAM6012_003193, gnl|extdb|FAM6012_003200, gnl|extdb|FAM6012_003203, gnl|extdb|FAM6012_003234, gnl|extdb|FAM6012_003262, gnl|extdb|FAM6012_003279, gnl|extdb|FAM6012_003291, gnl|extdb|FAM6012_003294 gnl|extdb|FAM6161_000297, gnl|extdb|FAM6161_000304, gnl|extdb|FAM6161_000336, gnl|extdb|FAM6161_001404 gnl|extdb|FAM6165_000006, gnl|extdb|FAM6165_000021, gnl|extdb|FAM6165_000160, gnl|extdb|FAM6165_000168, gnl|extdb|FAM6165_000175, gnl|extdb|FAM6165_000274, gnl|extdb|FAM6165_001006, gnl|extdb|FAM6165_002118, gnl|extdb|FAM6165_002562, gnl|extdb|FAM6165_002812, gnl|extdb|FAM6165_002830, gnl|extdb|FAM6165_002853, gnl|extdb|FAM6165_002867, 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gnl|extdb|FAM8374_000512, gnl|extdb|FAM8374_000672, gnl|extdb|FAM8374_001038, gnl|extdb|FAM8374_001380, gnl|extdb|FAM8374_002076, gnl|extdb|FAM8374_002525, gnl|extdb|FAM8374_002526, gnl|extdb|FAM8374_003146, gnl|extdb|FAM8374_003173, gnl|extdb|FAM8374_003218, gnl|extdb|FAM8374_003226, gnl|extdb|FAM8374_003248, gnl|extdb|FAM8374_003250 gnl|extdb|FAM8407_000302, gnl|extdb|FAM8407_000721, gnl|extdb|FAM8407_000728, gnl|extdb|FAM8407_003035 -OG0000001 gnl|extdb|FAM10859_000374, gnl|extdb|FAM10859_002725 gnl|extdb|FAM18099_000005, gnl|extdb|FAM18099_000116, gnl|extdb|FAM18099_000148, gnl|extdb|FAM18099_000380, gnl|extdb|FAM18099_000500, gnl|extdb|FAM18099_000795, gnl|extdb|FAM18099_001025, gnl|extdb|FAM18099_001316, gnl|extdb|FAM18099_001812, gnl|extdb|FAM18099_001828, gnl|extdb|FAM18099_001909, gnl|extdb|FAM18099_002086, gnl|extdb|FAM18099_002153, gnl|extdb|FAM18099_002490, gnl|extdb|FAM18099_002608, gnl|extdb|FAM18099_002853, gnl|extdb|FAM18099_002894, gnl|extdb|FAM18099_003023, 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gnl|extdb|FAM3257_002629 gnl|extdb|FAM8374_002636 -OG0004173 gnl|extdb|FAM3257_003045 gnl|extdb|FAM8374_003072 -OG0004174 gnl|extdb|FAM3257_003079 gnl|extdb|FAM8374_000029 -OG0004175 gnl|extdb|FAM3257_003342 gnl|extdb|FAM6165_003012 -OG0004176 gnl|extdb|FAM6012_001851 gnl|extdb|FAM8407_001421 -OG0004177 gnl|extdb|FAM6012_001852 gnl|extdb|FAM8407_001420 -OG0004178 gnl|extdb|FAM6012_002389 gnl|extdb|FAM6165_002243 -OG0004179 gnl|extdb|FAM6012_003134 gnl|extdb|FAM6165_000233 -OG0004180 gnl|extdb|FAM6161_000698 gnl|extdb|FAM7821_002636 -OG0004181 gnl|extdb|FAM6161_000782 gnl|extdb|FAM7821_002059 -OG0004182 gnl|extdb|FAM6161_000783 gnl|extdb|FAM7821_002060 -OG0004183 gnl|extdb|FAM6161_000978 gnl|extdb|FAM7821_002258 -OG0004184 gnl|extdb|FAM6161_000996 gnl|extdb|FAM7821_002278 -OG0004185 gnl|extdb|FAM6161_000997 gnl|extdb|FAM7821_002279 -OG0004186 gnl|extdb|FAM6161_001007 gnl|extdb|FAM7821_002289 -OG0004187 gnl|extdb|FAM6161_001055 gnl|extdb|FAM7821_002339 -OG0004188 gnl|extdb|FAM6161_001074 gnl|extdb|FAM7821_002360 -OG0004189 gnl|extdb|FAM6161_001075 gnl|extdb|FAM7821_002361 -OG0004190 gnl|extdb|FAM6161_001076 gnl|extdb|FAM7821_002362 -OG0004191 gnl|extdb|FAM6161_001256 gnl|extdb|FAM7821_002543 -OG0004192 gnl|extdb|FAM6161_001212 gnl|extdb|FAM7821_002499 -OG0004193 gnl|extdb|FAM6161_001292 gnl|extdb|FAM7821_002714 -OG0004194 gnl|extdb|FAM6161_001456 gnl|extdb|FAM7821_002878 -OG0004195 gnl|extdb|FAM6161_001457 gnl|extdb|FAM7821_002879 -OG0004196 gnl|extdb|FAM6161_001499 gnl|extdb|FAM7821_002921 -OG0004197 gnl|extdb|FAM6161_001500 gnl|extdb|FAM7821_002922 -OG0004198 gnl|extdb|FAM6161_001497 gnl|extdb|FAM7821_002919 -OG0004199 gnl|extdb|FAM6161_001777 gnl|extdb|FAM7821_000052 -OG0004200 gnl|extdb|FAM6161_001846 gnl|extdb|FAM7821_000122 -OG0004201 gnl|extdb|FAM6161_001917 gnl|extdb|FAM7821_000194 -OG0004202 gnl|extdb|FAM6161_003142 gnl|extdb|FAM6165_002209 -OG0004203 gnl|extdb|FAM6410_003272 gnl|extdb|FAM8374_003176 +Orthogroup FAM1079-i1-1.1 FAM13496-i1-1.1 FAM14217-p1-1.1 FAM17891-i1-1.1 FAM17927-i1-1.1 FAM18356-i1-1.1 FAM18815-i1-1.1 FAM18969-i1-1.1 FAM19036-p1-1.1 FAM19038-p1-1.1 FAM19144-i1-1.1 FAM19471-i1-1.1 FAM20446-i1-1.1 FAM20558-i1-1.1 FAM20833-i1-1.1 FAM21277-i1-1.1 FAM21784-i1-1.1 FAM21789-i1-1.1 FAM22472-i1-1.1 FAM23169-i1-1.1 FAM23217-i1-1.1 FAM24227-i1-1.1 FAM24235-i1-1.1 FAM3257-i1-1.1 +OG0000000 gnl|extdb|FAM1079-i1-1.1_000069, gnl|extdb|FAM1079-i1-1.1_000128, gnl|extdb|FAM1079-i1-1.1_000137, gnl|extdb|FAM1079-i1-1.1_000370, gnl|extdb|FAM1079-i1-1.1_000660, gnl|extdb|FAM1079-i1-1.1_000743, gnl|extdb|FAM1079-i1-1.1_000785, gnl|extdb|FAM1079-i1-1.1_000846, gnl|extdb|FAM1079-i1-1.1_000876, gnl|extdb|FAM1079-i1-1.1_001225, gnl|extdb|FAM1079-i1-1.1_001413, gnl|extdb|FAM1079-i1-1.1_001658, gnl|extdb|FAM1079-i1-1.1_001679, gnl|extdb|FAM1079-i1-1.1_001721, gnl|extdb|FAM1079-i1-1.1_001768, gnl|extdb|FAM1079-i1-1.1_001814, gnl|extdb|FAM1079-i1-1.1_001855, gnl|extdb|FAM1079-i1-1.1_001872, gnl|extdb|FAM1079-i1-1.1_001898, 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gnl|extdb|FAM17927-i1-1.1_000171, gnl|extdb|FAM17927-i1-1.1_000177, gnl|extdb|FAM17927-i1-1.1_000204, gnl|extdb|FAM17927-i1-1.1_000256, gnl|extdb|FAM17927-i1-1.1_000688, gnl|extdb|FAM17927-i1-1.1_001250, gnl|extdb|FAM17927-i1-1.1_001304, gnl|extdb|FAM17927-i1-1.1_001762, gnl|extdb|FAM17927-i1-1.1_001803, gnl|extdb|FAM17927-i1-1.1_001837, gnl|extdb|FAM17927-i1-1.1_002285, gnl|extdb|FAM17927-i1-1.1_002724 gnl|extdb|FAM18356-i1-1.1_000116, gnl|extdb|FAM18356-i1-1.1_000119, gnl|extdb|FAM18356-i1-1.1_000173, gnl|extdb|FAM18356-i1-1.1_000184, gnl|extdb|FAM18356-i1-1.1_000227, gnl|extdb|FAM18356-i1-1.1_000321, gnl|extdb|FAM18356-i1-1.1_000371, gnl|extdb|FAM18356-i1-1.1_000808, gnl|extdb|FAM18356-i1-1.1_000834, gnl|extdb|FAM18356-i1-1.1_000870, gnl|extdb|FAM18356-i1-1.1_001324, gnl|extdb|FAM18356-i1-1.1_001583, gnl|extdb|FAM18356-i1-1.1_001895 gnl|extdb|FAM18815-i1-1.1_000068, gnl|extdb|FAM18815-i1-1.1_000141, gnl|extdb|FAM18815-i1-1.1_000207, gnl|extdb|FAM18815-i1-1.1_000217, gnl|extdb|FAM18815-i1-1.1_000300, gnl|extdb|FAM18815-i1-1.1_000327, gnl|extdb|FAM18815-i1-1.1_000455, gnl|extdb|FAM18815-i1-1.1_000483, gnl|extdb|FAM18815-i1-1.1_000573, gnl|extdb|FAM18815-i1-1.1_000604, gnl|extdb|FAM18815-i1-1.1_000676, gnl|extdb|FAM18815-i1-1.1_001147, gnl|extdb|FAM18815-i1-1.1_001178, gnl|extdb|FAM18815-i1-1.1_001195, gnl|extdb|FAM18815-i1-1.1_001336, gnl|extdb|FAM18815-i1-1.1_001548, gnl|extdb|FAM18815-i1-1.1_001755 gnl|extdb|FAM18969-i1-1.1_000234, gnl|extdb|FAM18969-i1-1.1_000329, gnl|extdb|FAM18969-i1-1.1_000351, gnl|extdb|FAM18969-i1-1.1_000749, gnl|extdb|FAM18969-i1-1.1_000886, gnl|extdb|FAM18969-i1-1.1_000923, gnl|extdb|FAM18969-i1-1.1_001047, gnl|extdb|FAM18969-i1-1.1_001072, gnl|extdb|FAM18969-i1-1.1_001123, gnl|extdb|FAM18969-i1-1.1_001361, gnl|extdb|FAM18969-i1-1.1_001388, gnl|extdb|FAM18969-i1-1.1_001714, gnl|extdb|FAM18969-i1-1.1_001724, gnl|extdb|FAM18969-i1-1.1_001929, gnl|extdb|FAM18969-i1-1.1_001995 gnl|extdb|FAM19036-p1-1.1_000114, gnl|extdb|FAM19036-p1-1.1_000189, gnl|extdb|FAM19036-p1-1.1_000223, gnl|extdb|FAM19036-p1-1.1_000395, gnl|extdb|FAM19036-p1-1.1_000436, gnl|extdb|FAM19036-p1-1.1_000442, gnl|extdb|FAM19036-p1-1.1_000523, gnl|extdb|FAM19036-p1-1.1_000592, gnl|extdb|FAM19036-p1-1.1_000757, gnl|extdb|FAM19036-p1-1.1_000871, gnl|extdb|FAM19036-p1-1.1_000936, gnl|extdb|FAM19036-p1-1.1_001147, gnl|extdb|FAM19036-p1-1.1_001280, gnl|extdb|FAM19036-p1-1.1_001795, gnl|extdb|FAM19036-p1-1.1_001804, gnl|extdb|FAM19036-p1-1.1_001927, gnl|extdb|FAM19036-p1-1.1_001935, gnl|extdb|FAM19036-p1-1.1_001984, gnl|extdb|FAM19036-p1-1.1_002262, gnl|extdb|FAM19036-p1-1.1_002270, gnl|extdb|FAM19036-p1-1.1_002352, gnl|extdb|FAM19036-p1-1.1_002424, gnl|extdb|FAM19036-p1-1.1_002657, gnl|extdb|FAM19036-p1-1.1_002916, gnl|extdb|FAM19036-p1-1.1_003032, gnl|extdb|FAM19036-p1-1.1_003076, gnl|extdb|FAM19036-p1-1.1_003235, gnl|extdb|FAM19036-p1-1.1_003319, gnl|extdb|FAM19036-p1-1.1_003326 gnl|extdb|FAM19038-p1-1.1_000040, gnl|extdb|FAM19038-p1-1.1_000046, gnl|extdb|FAM19038-p1-1.1_000129, gnl|extdb|FAM19038-p1-1.1_000190, gnl|extdb|FAM19038-p1-1.1_000197, gnl|extdb|FAM19038-p1-1.1_000483, gnl|extdb|FAM19038-p1-1.1_000523, gnl|extdb|FAM19038-p1-1.1_000713, gnl|extdb|FAM19038-p1-1.1_000847, gnl|extdb|FAM19038-p1-1.1_000983, gnl|extdb|FAM19038-p1-1.1_001004, gnl|extdb|FAM19038-p1-1.1_001032, gnl|extdb|FAM19038-p1-1.1_001065, gnl|extdb|FAM19038-p1-1.1_001091, gnl|extdb|FAM19038-p1-1.1_001191, gnl|extdb|FAM19038-p1-1.1_001350, gnl|extdb|FAM19038-p1-1.1_001392, gnl|extdb|FAM19038-p1-1.1_001481, gnl|extdb|FAM19038-p1-1.1_001531, gnl|extdb|FAM19038-p1-1.1_001688, gnl|extdb|FAM19038-p1-1.1_001874, gnl|extdb|FAM19038-p1-1.1_001911, gnl|extdb|FAM19038-p1-1.1_002073, gnl|extdb|FAM19038-p1-1.1_002249, gnl|extdb|FAM19038-p1-1.1_002382, gnl|extdb|FAM19038-p1-1.1_002616 gnl|extdb|FAM19144-i1-1.1_000223, gnl|extdb|FAM19144-i1-1.1_000276, gnl|extdb|FAM19144-i1-1.1_000302, gnl|extdb|FAM19144-i1-1.1_000509, 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gnl|extdb|FAM18969-i1-1.1_000966, gnl|extdb|FAM18969-i1-1.1_001957 gnl|extdb|FAM19036-p1-1.1_000154, gnl|extdb|FAM19036-p1-1.1_001562, gnl|extdb|FAM19036-p1-1.1_002496, gnl|extdb|FAM19036-p1-1.1_002497, gnl|extdb|FAM19036-p1-1.1_002709 gnl|extdb|FAM19038-p1-1.1_000544, gnl|extdb|FAM19038-p1-1.1_000545, gnl|extdb|FAM19038-p1-1.1_001160, gnl|extdb|FAM19038-p1-1.1_002487 gnl|extdb|FAM19144-i1-1.1_000376, gnl|extdb|FAM19144-i1-1.1_001195, gnl|extdb|FAM19144-i1-1.1_001210 gnl|extdb|FAM19471-i1-1.1_000734, gnl|extdb|FAM19471-i1-1.1_001128 gnl|extdb|FAM20446-i1-1.1_002240, gnl|extdb|FAM20446-i1-1.1_002308 gnl|extdb|FAM20558-i1-1.1_001408, gnl|extdb|FAM20558-i1-1.1_001932 gnl|extdb|FAM20833-i1-1.1_000786 gnl|extdb|FAM21277-i1-1.1_001788, gnl|extdb|FAM21277-i1-1.1_002064 gnl|extdb|FAM21784-i1-1.1_000176, gnl|extdb|FAM21784-i1-1.1_000294, gnl|extdb|FAM21784-i1-1.1_001566 gnl|extdb|FAM21789-i1-1.1_002683, gnl|extdb|FAM21789-i1-1.1_002769, gnl|extdb|FAM21789-i1-1.1_003029 gnl|extdb|FAM22472-i1-1.1_000298, gnl|extdb|FAM22472-i1-1.1_000299, gnl|extdb|FAM22472-i1-1.1_000647, gnl|extdb|FAM22472-i1-1.1_001520, gnl|extdb|FAM22472-i1-1.1_001774 gnl|extdb|FAM23169-i1-1.1_000629, gnl|extdb|FAM23169-i1-1.1_001536 gnl|extdb|FAM23217-i1-1.1_000624, gnl|extdb|FAM23217-i1-1.1_000745, gnl|extdb|FAM23217-i1-1.1_000928 gnl|extdb|FAM24227-i1-1.1_001190, gnl|extdb|FAM24227-i1-1.1_001364, gnl|extdb|FAM24227-i1-1.1_002180 gnl|extdb|FAM24235-i1-1.1_000678, gnl|extdb|FAM24235-i1-1.1_001791 gnl|extdb|FAM3257-i1-1.1_000293, gnl|extdb|FAM3257-i1-1.1_002658 +OG0000038 gnl|extdb|FAM1079-i1-1.1_001744 gnl|extdb|FAM14217-p1-1.1_000267 gnl|extdb|FAM17891-i1-1.1_000030, gnl|extdb|FAM17891-i1-1.1_001339, gnl|extdb|FAM17891-i1-1.1_002097 gnl|extdb|FAM17927-i1-1.1_000030, gnl|extdb|FAM17927-i1-1.1_001339, gnl|extdb|FAM17927-i1-1.1_002097 gnl|extdb|FAM18815-i1-1.1_001187 gnl|extdb|FAM19036-p1-1.1_000038, gnl|extdb|FAM19036-p1-1.1_000050, gnl|extdb|FAM19036-p1-1.1_000059, 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gnl|extdb|FAM20558-i1-1.1_001807, gnl|extdb|FAM20558-i1-1.1_001973 gnl|extdb|FAM20833-i1-1.1_000759 gnl|extdb|FAM21277-i1-1.1_000298, gnl|extdb|FAM21277-i1-1.1_001180 gnl|extdb|FAM21784-i1-1.1_001425, gnl|extdb|FAM21784-i1-1.1_001866 gnl|extdb|FAM21789-i1-1.1_000691, gnl|extdb|FAM21789-i1-1.1_001280, gnl|extdb|FAM21789-i1-1.1_001810, gnl|extdb|FAM21789-i1-1.1_002411, gnl|extdb|FAM21789-i1-1.1_002531 gnl|extdb|FAM22472-i1-1.1_000395 gnl|extdb|FAM23169-i1-1.1_000989 gnl|extdb|FAM23217-i1-1.1_000437, gnl|extdb|FAM23217-i1-1.1_001356 gnl|extdb|FAM24227-i1-1.1_001154, gnl|extdb|FAM24227-i1-1.1_001881 gnl|extdb|FAM24235-i1-1.1_001692, gnl|extdb|FAM24235-i1-1.1_002378 gnl|extdb|FAM3257-i1-1.1_000530, gnl|extdb|FAM3257-i1-1.1_000694, gnl|extdb|FAM3257-i1-1.1_003156 +OG0000071 gnl|extdb|FAM1079-i1-1.1_001746, gnl|extdb|FAM1079-i1-1.1_001785 gnl|extdb|FAM13496-i1-1.1_000499 gnl|extdb|FAM14217-p1-1.1_000594, gnl|extdb|FAM14217-p1-1.1_000869 gnl|extdb|FAM17891-i1-1.1_000075, 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gnl|extdb|FAM20833-i1-1.1_000471 gnl|extdb|FAM21277-i1-1.1_000056, gnl|extdb|FAM21277-i1-1.1_001943 gnl|extdb|FAM21784-i1-1.1_000428, gnl|extdb|FAM21784-i1-1.1_001739 gnl|extdb|FAM21789-i1-1.1_002250 gnl|extdb|FAM22472-i1-1.1_001763 gnl|extdb|FAM23169-i1-1.1_000450, gnl|extdb|FAM23169-i1-1.1_001066 gnl|extdb|FAM23217-i1-1.1_001673 gnl|extdb|FAM24227-i1-1.1_001508, gnl|extdb|FAM24227-i1-1.1_002007, gnl|extdb|FAM24227-i1-1.1_002345, gnl|extdb|FAM24227-i1-1.1_002399 gnl|extdb|FAM24235-i1-1.1_000068, gnl|extdb|FAM24235-i1-1.1_000604 gnl|extdb|FAM3257-i1-1.1_001543, gnl|extdb|FAM3257-i1-1.1_001808, gnl|extdb|FAM3257-i1-1.1_001926 +OG0000099 gnl|extdb|FAM1079-i1-1.1_000107, gnl|extdb|FAM1079-i1-1.1_002552 gnl|extdb|FAM21277-i1-1.1_000450, gnl|extdb|FAM21277-i1-1.1_001061, gnl|extdb|FAM21277-i1-1.1_001107, gnl|extdb|FAM21277-i1-1.1_001553, gnl|extdb|FAM21277-i1-1.1_001567, gnl|extdb|FAM21277-i1-1.1_001822, gnl|extdb|FAM21277-i1-1.1_002026, gnl|extdb|FAM21277-i1-1.1_002088, 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gnl|extdb|FAM21784-i1-1.1_000283 gnl|extdb|FAM21789-i1-1.1_000194, gnl|extdb|FAM21789-i1-1.1_001070, gnl|extdb|FAM21789-i1-1.1_001335, gnl|extdb|FAM21789-i1-1.1_001955, gnl|extdb|FAM21789-i1-1.1_002487, gnl|extdb|FAM21789-i1-1.1_002685, gnl|extdb|FAM21789-i1-1.1_003234 gnl|extdb|FAM22472-i1-1.1_000531 gnl|extdb|FAM23169-i1-1.1_000965, gnl|extdb|FAM23169-i1-1.1_000974, gnl|extdb|FAM23169-i1-1.1_001402 gnl|extdb|FAM3257-i1-1.1_001160, gnl|extdb|FAM3257-i1-1.1_002077, gnl|extdb|FAM3257-i1-1.1_002336 +OG0000149 gnl|extdb|FAM1079-i1-1.1_001420, gnl|extdb|FAM1079-i1-1.1_001930, gnl|extdb|FAM1079-i1-1.1_002239 gnl|extdb|FAM13496-i1-1.1_000623 gnl|extdb|FAM14217-p1-1.1_000554, gnl|extdb|FAM14217-p1-1.1_001296, gnl|extdb|FAM14217-p1-1.1_001709 gnl|extdb|FAM17891-i1-1.1_001066 gnl|extdb|FAM17927-i1-1.1_001066 gnl|extdb|FAM18356-i1-1.1_000300, gnl|extdb|FAM18356-i1-1.1_000866 gnl|extdb|FAM18815-i1-1.1_000303 gnl|extdb|FAM19036-p1-1.1_000125, gnl|extdb|FAM19036-p1-1.1_000795, 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gnl|extdb|FAM13496-i1-1.1_001239 gnl|extdb|FAM17891-i1-1.1_000130, gnl|extdb|FAM17891-i1-1.1_001450, gnl|extdb|FAM17891-i1-1.1_002655 gnl|extdb|FAM17927-i1-1.1_000130, gnl|extdb|FAM17927-i1-1.1_001450, gnl|extdb|FAM17927-i1-1.1_002655 gnl|extdb|FAM18815-i1-1.1_000194, gnl|extdb|FAM18815-i1-1.1_000262 gnl|extdb|FAM19144-i1-1.1_000923 gnl|extdb|FAM19471-i1-1.1_000821 gnl|extdb|FAM20446-i1-1.1_000777, gnl|extdb|FAM20446-i1-1.1_002184, gnl|extdb|FAM20446-i1-1.1_002863 gnl|extdb|FAM20558-i1-1.1_000093, gnl|extdb|FAM20558-i1-1.1_000643, gnl|extdb|FAM20558-i1-1.1_002482 gnl|extdb|FAM21277-i1-1.1_000335 gnl|extdb|FAM21784-i1-1.1_000615 gnl|extdb|FAM21789-i1-1.1_000052, gnl|extdb|FAM21789-i1-1.1_001288, gnl|extdb|FAM21789-i1-1.1_002454 gnl|extdb|FAM22472-i1-1.1_000835 gnl|extdb|FAM23217-i1-1.1_000075, gnl|extdb|FAM23217-i1-1.1_000184, gnl|extdb|FAM23217-i1-1.1_002095 gnl|extdb|FAM24227-i1-1.1_000029, gnl|extdb|FAM24227-i1-1.1_001839 gnl|extdb|FAM24235-i1-1.1_000943 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gnl|extdb|FAM24235-i1-1.1_001715 +OG0005977 gnl|extdb|FAM24235-i1-1.1_000518, gnl|extdb|FAM24235-i1-1.1_000519 +OG0005978 gnl|extdb|FAM24235-i1-1.1_000556, gnl|extdb|FAM24235-i1-1.1_001266 +OG0005979 gnl|extdb|FAM24235-i1-1.1_000568, gnl|extdb|FAM24235-i1-1.1_002411 +OG0005980 gnl|extdb|FAM24235-i1-1.1_000711, gnl|extdb|FAM24235-i1-1.1_001501 +OG0005981 gnl|extdb|FAM24235-i1-1.1_000713, gnl|extdb|FAM24235-i1-1.1_001503 +OG0005982 gnl|extdb|FAM24235-i1-1.1_000714, gnl|extdb|FAM24235-i1-1.1_001504 +OG0005983 gnl|extdb|FAM24235-i1-1.1_000719, gnl|extdb|FAM24235-i1-1.1_001505 +OG0005984 gnl|extdb|FAM24235-i1-1.1_000839, gnl|extdb|FAM24235-i1-1.1_002144 +OG0005985 gnl|extdb|FAM24235-i1-1.1_000995, gnl|extdb|FAM24235-i1-1.1_001803 +OG0005986 gnl|extdb|FAM24235-i1-1.1_001039, gnl|extdb|FAM24235-i1-1.1_001407 +OG0005987 gnl|extdb|FAM24235-i1-1.1_001118, gnl|extdb|FAM24235-i1-1.1_002794 +OG0005988 gnl|extdb|FAM24235-i1-1.1_001133, gnl|extdb|FAM24235-i1-1.1_001151 +OG0005989 gnl|extdb|FAM24235-i1-1.1_001254, gnl|extdb|FAM24235-i1-1.1_002409 +OG0005990 gnl|extdb|FAM24235-i1-1.1_001285, gnl|extdb|FAM24235-i1-1.1_002840 +OG0005991 gnl|extdb|FAM24235-i1-1.1_001405, gnl|extdb|FAM24235-i1-1.1_002309 +OG0005992 gnl|extdb|FAM24235-i1-1.1_001553, gnl|extdb|FAM24235-i1-1.1_001693 +OG0005993 gnl|extdb|FAM24235-i1-1.1_001613, gnl|extdb|FAM24235-i1-1.1_001614 +OG0005994 gnl|extdb|FAM24235-i1-1.1_001637 gnl|extdb|FAM3257-i1-1.1_003102 +OG0005995 gnl|extdb|FAM24235-i1-1.1_001640 gnl|extdb|FAM3257-i1-1.1_003105 +OG0005996 gnl|extdb|FAM24235-i1-1.1_001998, gnl|extdb|FAM24235-i1-1.1_002096 +OG0005997 gnl|extdb|FAM24235-i1-1.1_002109, gnl|extdb|FAM24235-i1-1.1_002650 +OG0005998 gnl|extdb|FAM24235-i1-1.1_002120, gnl|extdb|FAM24235-i1-1.1_002121 +OG0005999 gnl|extdb|FAM24235-i1-1.1_002256, gnl|extdb|FAM24235-i1-1.1_002259 +OG0006000 gnl|extdb|FAM24235-i1-1.1_002277 gnl|extdb|FAM3257-i1-1.1_002138 +OG0006001 gnl|extdb|FAM24235-i1-1.1_002278 gnl|extdb|FAM3257-i1-1.1_002137 +OG0006002 gnl|extdb|FAM24235-i1-1.1_002281 gnl|extdb|FAM3257-i1-1.1_002134 +OG0006003 gnl|extdb|FAM24235-i1-1.1_002372, gnl|extdb|FAM24235-i1-1.1_002390 +OG0006004 gnl|extdb|FAM24235-i1-1.1_002497 gnl|extdb|FAM3257-i1-1.1_000291 +OG0006005 gnl|extdb|FAM24235-i1-1.1_002557, gnl|extdb|FAM24235-i1-1.1_002558 +OG0006006 gnl|extdb|FAM24235-i1-1.1_002565, gnl|extdb|FAM24235-i1-1.1_002566 +OG0006007 gnl|extdb|FAM24235-i1-1.1_002571, gnl|extdb|FAM24235-i1-1.1_002774 +OG0006008 gnl|extdb|FAM24235-i1-1.1_002693, gnl|extdb|FAM24235-i1-1.1_002704 +OG0006009 gnl|extdb|FAM24235-i1-1.1_002694, gnl|extdb|FAM24235-i1-1.1_002705 +OG0006010 gnl|extdb|FAM24235-i1-1.1_002695, gnl|extdb|FAM24235-i1-1.1_002706 +OG0006011 gnl|extdb|FAM24235-i1-1.1_002809, gnl|extdb|FAM24235-i1-1.1_002830 +OG0006012 gnl|extdb|FAM24235-i1-1.1_002823, gnl|extdb|FAM24235-i1-1.1_002824 +OG0006013 gnl|extdb|FAM3257-i1-1.1_000404, gnl|extdb|FAM3257-i1-1.1_003057 +OG0006014 gnl|extdb|FAM3257-i1-1.1_000439, gnl|extdb|FAM3257-i1-1.1_000860 +OG0006015 gnl|extdb|FAM3257-i1-1.1_000477, gnl|extdb|FAM3257-i1-1.1_000577 +OG0006016 gnl|extdb|FAM3257-i1-1.1_000598, gnl|extdb|FAM3257-i1-1.1_002826 +OG0006017 gnl|extdb|FAM3257-i1-1.1_000601, gnl|extdb|FAM3257-i1-1.1_002830 +OG0006018 gnl|extdb|FAM3257-i1-1.1_001021, gnl|extdb|FAM3257-i1-1.1_002182 +OG0006019 gnl|extdb|FAM3257-i1-1.1_001033, gnl|extdb|FAM3257-i1-1.1_002172 +OG0006020 gnl|extdb|FAM3257-i1-1.1_001037, gnl|extdb|FAM3257-i1-1.1_002169 +OG0006021 gnl|extdb|FAM3257-i1-1.1_002293, gnl|extdb|FAM3257-i1-1.1_002313 +OG0006022 gnl|extdb|FAM3257-i1-1.1_003033, gnl|extdb|FAM3257-i1-1.1_003041 +OG0006023 gnl|extdb|FAM3257-i1-1.1_003034, gnl|extdb|FAM3257-i1-1.1_003042 diff --git a/data/SpeciesTree_rooted.txt b/data/SpeciesTree_rooted.txt index dbdd4f2..2de3e67 100644 --- a/data/SpeciesTree_rooted.txt +++ b/data/SpeciesTree_rooted.txt @@ -1 +1 @@ -(FAM6410:0.00028,((FAM6161:0.00055,FAM7821:0.00055):0.00197,((FAM23967:0.00055,(FAM23966:0.00055,FAM8140:0.00055):0.00055):0.00054,(FAM18108:0.00084,((FAM3228:0,FAM19353:0):1,((FAM3257:0.00066,FAM8374:0.00053):0.00187,((FAM22277:0.00197,(FAM18099:0.00183,(FAM4067:0.00054,(FAM10859:0.00054,(FAM22276:0,FAM3248:0):1):0.00055):0.00084):0.00071):0.00055,((FAM18121:0.0029,(FAM18119:0.00187,(FAM18157:0.00123,(FAM6012:0.00072,((FAM22278:0.00074,(FAM18113:0.00096,((FAM23965:0,FAM23964:0):1,(FAM6165:0.00093,(FAM18168:0,FAM18149:0,FAM22437:0,FAM22436:0):1):0.00055):0.00055):0.00055):0.00055,(FAM22280:0.00129,(FAM18132:0.00055,(FAM18101:0.00055,FAM18105:0.00055):0.00055):0.00095):0.00055):0.00055):0.00079):0.0012):0.00058):0.00093,((FAM8407:0.002,(FAM19404:0.002,(FAM18172:0.00088,(FAM18123:0.00066,(FAM18110:0.00096,FAM22279:0.00075):0.00055):0.00055):0.00055):0.00057):0.00055,((FAM18126:0.00161,(FAM18129:0.00055,FAM18124:0.00055):0.00108):0.00105,FAM18175:0.00144):0.00061):0.00099):0.00055):1):0.0006):0.00102):0.00083):0.00064):0.00028); \ No newline at end of file +((((FAM24235-i1-1.1:0.253458,FAM24227-i1-1.1:0.317407)0.377644:0.044094,(FAM20833-i1-1.1:0.362562,(FAM14217-p1-1.1:0.260305,(FAM19038-p1-1.1:0.100324,FAM19036-p1-1.1:0.0972652)0.975831:0.163879)0.975831:0.575651)0.401813:0.0707424)0.208459:0.0338095,(FAM13496-i1-1.1:0.201101,((FAM17927-i1-1.1:5.28266e-06,FAM17891-i1-1.1:5.28266e-06)0.996979:0.180079,FAM23217-i1-1.1:0.162842)0.610272:0.0643953)0.885196:0.118739)0.444109:0.0224931,(((FAM3257-i1-1.1:0.031946,(FAM20446-i1-1.1:0.0263137,FAM20558-i1-1.1:0.0236257)0.73716:0.0161983)0.987915:0.191205,(FAM22472-i1-1.1:0.150239,(FAM21784-i1-1.1:0.00293131,FAM21277-i1-1.1:0.00290364)0.990937:0.151356)0.915408:0.160942)0.268882:0.0373102,(FAM18356-i1-1.1:0.30985,(((FAM23169-i1-1.1:0.0778526,FAM1079-i1-1.1:0.0796974)0.978852:0.120403,(FAM21789-i1-1.1:0.169698,(FAM18969-i1-1.1:0.0766641,(FAM19144-i1-1.1:0.0573283,FAM18815-i1-1.1:0.0587491)0.770393:0.0259417)0.963746:0.128755)0.238671:0.0197277)0.256798:0.0239291,FAM19471-i1-1.1:0.223007)0.293051:0.0258009)0.217523:0.0386439)0.444109:0.0224931); \ No newline at end of file diff --git a/data/SpeciesTree_rooted_node_labels.txt b/data/SpeciesTree_rooted_node_labels.txt index 053dee3..3e60031 100644 --- a/data/SpeciesTree_rooted_node_labels.txt +++ b/data/SpeciesTree_rooted_node_labels.txt @@ -1 +1 @@ -(FAM6410:0.00028,((FAM6161:0.00055,FAM7821:0.00055)N2:0.00197,((FAM23967:0.00055,(FAM23966:0.00055,FAM8140:0.00055)N6:0.00055)N4:0.00054,(FAM18108:0.00084,((FAM3228:0,FAM19353:0)N8:1,((FAM3257:0.00066,FAM8374:0.00053)N10:0.00187,((FAM22277:0.00197,(FAM18099:0.00183,(FAM4067:0.00054,(FAM10859:0.00054,(FAM22276:0,FAM3248:0)N25:1)N21:0.00055)N17:0.00084)N14:0.00071)N12:0.00055,((FAM18121:0.0029,(FAM18119:0.00187,(FAM18157:0.00123,(FAM6012:0.00072,((FAM22278:0.00074,(FAM18113:0.00096,((FAM23965:0,FAM23964:0)N38:1,(FAM6165:0.00093,(FAM18168:0,FAM18149:0,FAM22437:0,FAM22436:0)N40:1)N39:0.00055)N36:0.00055)N34:0.00055)N31:0.00055,(FAM22280:0.00129,(FAM18132:0.00055,(FAM18101:0.00055,FAM18105:0.00055)N37:0.00055)N35:0.00095)N32:0.00055)N29:0.00055)N26:0.00079)N22:0.0012)N18:0.00058)N15:0.00093,((FAM8407:0.002,(FAM19404:0.002,(FAM18172:0.00088,(FAM18123:0.00066,(FAM18110:0.00096,FAM22279:0.00075)N33:0.00055)N30:0.00055)N27:0.00055)N23:0.00057)N19:0.00055,((FAM18126:0.00161,(FAM18129:0.00055,FAM18124:0.00055)N28:0.00108)N24:0.00105,FAM18175:0.00144)N20:0.00061)N16:0.00099)N13:0.00055)N11:1)N9:0.0006)N7:0.00102)N5:0.00083)N3:0.00064)N1:0.00028)N0; \ No newline at end of file +((((FAM24235-i1-1.1:0.253458,FAM24227-i1-1.1:0.317407)N7:0.044094,(FAM20833-i1-1.1:0.362562,(FAM14217-p1-1.1:0.260305,(FAM19038-p1-1.1:0.100324,FAM19036-p1-1.1:0.0972652)N18:0.163879)N13:0.575651)N8:0.0707424)N3:0.0338095,(FAM13496-i1-1.1:0.201101,((FAM17927-i1-1.1:5.28266e-06,FAM17891-i1-1.1:5.28266e-06)N14:0.180079,FAM23217-i1-1.1:0.162842)N9:0.0643953)N4:0.118739)N1:0.0224931,(((FAM3257-i1-1.1:0.031946,(FAM20446-i1-1.1:0.0263137,FAM20558-i1-1.1:0.0236257)N15:0.0161983)N10:0.191205,(FAM22472-i1-1.1:0.150239,(FAM21784-i1-1.1:0.00293131,FAM21277-i1-1.1:0.00290364)N16:0.151356)N11:0.160942)N5:0.0373102,(FAM18356-i1-1.1:0.30985,(((FAM23169-i1-1.1:0.0778526,FAM1079-i1-1.1:0.0796974)N19:0.120403,(FAM21789-i1-1.1:0.169698,(FAM18969-i1-1.1:0.0766641,(FAM19144-i1-1.1:0.0573283,FAM18815-i1-1.1:0.0587491)N22:0.0259417)N21:0.128755)N20:0.0197277)N17:0.0239291,FAM19471-i1-1.1:0.223007)N12:0.0258009)N6:0.0386439)N2:0.0224931)N0; \ No newline at end of file diff --git a/orthogroup_to_gene_name.py b/orthogroup_to_gene_name.py index 234064c..087a56b 100644 --- a/orthogroup_to_gene_name.py +++ b/orthogroup_to_gene_name.py @@ -1,19 +1,23 @@ +#!/usr/bin/env python + import os import pandas as pd from Bio import SeqIO + class OrthogroupToGeneName(): @staticmethod - def run(orthogroups_tsv: str, fasta_dir: str, write: bool = False): + def run(orthogroups_tsv: str, fasta_dir: str, write: bool = True): + assert os.path.isfile(orthogroups_tsv), F'orthogroups_tsv does not exist: "{orthogroups_tsv}"' assert os.path.isdir(fasta_dir), F'fasta_dir does not exist: "{fasta_dir}"' if write: - out = os.path.dirname(orthogroups_tsv) + out = os.path.dirname("./result.tsv") assert os.path.isdir(out) - # read Orthogroups.tsv - df = pd.read_csv(orthogroups_tsv, sep='\t') - df.set_index('Orthogroup', inplace=True) + # read "N0.tsv" and drop extra columns + df = pd.read_csv(orthogroups_tsv, sep='\t').drop(columns=['OG', 'Gene Tree Parent Clade']) + df.set_index('HOG', inplace=True) def get_gene_name(identifer: str): identifer = identifer.split(' ', maxsplit=1)[1].split(' [', maxsplit=1)[0] @@ -26,14 +30,21 @@ def get_gene_id(identifer: str): return identifer.split(' ', maxsplit=1)[0] def get_gene_id_to_name_dict(strain): - fasta_file_path = os.path.join(fasta_dir + F'/{strain}.faa') + fasta_file_path = os.path.join(fasta_dir + F'/{strain}.fasta') assert os.path.isfile(fasta_file_path), F'fasta file "{fasta_file_path}" is missing!' genes = SeqIO.parse(fasta_file_path, "fasta") return {gene.id: gene.description.split(' ', maxsplit=1)[1] for gene in genes} def gene_id_to_gene_name(gene_ids, gene_id_to_name): if isinstance(gene_ids, float): return [] - return [gene_id_to_name[gene_id] for gene_id in gene_ids.split(', ')] + if gene_ids is None: return [] + + try: + return [gene_id_to_name[gene_id] for gene_id in gene_ids.split(', ')] + + except KeyError: + print("Genes not present in fasta file: \n", gene_ids) + return [] strains = df.columns for strain in strains: @@ -41,7 +52,12 @@ def gene_id_to_gene_name(gene_ids, gene_id_to_name): df[strain] = df[strain].apply(gene_id_to_gene_name, args=([gene_id_to_name])) def majority_vote(row, best_only=False): - all_names = [name for cell in row for name in cell] + """ Get gene names set per HOG and count them. Disregards names with eAED in description, + typically unusefull maker annotations""" + + all_names = [name for cell in row for name in cell if "eAED" not in name] + if not all_names: all_names = ["NO DESCRIPTION"] # if all names contain "eAED", all_names is an empty list + if best_only: return max(set(all_names), key=all_names.count) @@ -67,4 +83,4 @@ def majority_vote(row, best_only=False): if __name__ == "__main__": import fire # pip install fire # automated argparse - fire.Fire(OrthogroupToGeneName.run) + fire.Fire(OrthogroupToGeneName.run) \ No newline at end of file