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diff test-data/evidences.gff3 @ 1:1b3626164087 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398
author iuc
date Sun, 01 Jul 2018 16:12:07 -0400
parents 060ea7339911
children
line wrap: on
line diff
--- a/test-data/evidences.gff3	Thu Oct 19 15:59:20 2017 -0400
+++ b/test-data/evidences.gff3	Sun Jul 01 16:12:07 2018 -0400
@@ -1,62 +1,42 @@
 ##gff-version 3
 HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
 ###
-HS08198	repeatmasker	match	578	651	13	+	.	ID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +
-HS08198	repeatmasker	match_part	578	651	13	+	.	ID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +
-###
-HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:11:3.2.0.0;Name=HS08198.g2
-HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
-HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
-HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
-HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
-HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
-HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
-HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:12:3.2.0.0;Name=HS08198.g2
-HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:35:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
-HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:36:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
-HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
-HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
-HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
-HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:26:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:27:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
 HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
 ###
-HS04636	repeatmasker	match	9419	9435	16	+	.	ID=HS04636:hit:0:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 +
-HS04636	repeatmasker	match_part	9419	9435	16	+	.	ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
-HS04636	repeatmasker	match	939	980	13	+	.	ID=HS04636:hit:1:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match_part	939	980	13	+	.	ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match	3791	3839	22	+	.	ID=HS04636:hit:2:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match_part	3791	3839	22	+	.	ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match	6918	6977	17	+	.	ID=HS04636:hit:3:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match_part	6918	6977	17	+	.	ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match	6028	6072	21	+	.	ID=HS04636:hit:4:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match_part	6028	6072	21	+	.	ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match	4518	4541	17	+	.	ID=HS04636:hit:5:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 +
-HS04636	repeatmasker	match_part	4518	4541	17	+	.	ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
-HS04636	repeatmasker	match	3852	3888	12	+	.	ID=HS04636:hit:6:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match_part	3852	3888	12	+	.	ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:7:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +
-HS04636	repeatmasker	match_part	3840	3847	17	+	.	ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
-###
-HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:8:3.2.0.0;Name=HS04636.g1
-HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
-HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
-HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
-HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
-HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
-HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
-HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
-HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
-HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
-HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:9:3.2.0.0;Name=HS04636.g1
-HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
-HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
-HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
-HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
-HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
-HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
-HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
-HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
+HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1
+HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
+HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
+HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
+HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
+HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
+HS04636	blastn	match_part	4542	4790	249	+	.	ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 802 1050 +;Gap=M249
+HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
+HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
+HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
+HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1
+HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
+HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
+HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
+HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
+HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
+HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
+HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
+HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410