Mercurial > repos > greg > gene_family_classifier

changeset 150:8f2cd8053f78 draft

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Uploaded
author greg
date Tue, 06 Jun 2017 08:39:14 -0400
parents 8dd96fd18bbc
children 0864e87fbcd1
files gene_family_classifier.xml plant_tribes_scaffolds.loc repository_dependencies.xml test-data/output.ptorthocs test-data/proteins.blastp.22Gv1.1 test-data/proteins.blastp.22Gv1.1.bestOrthos test-data/proteins.blastp.22Gv1.1.bestOrthos.summary test-data/proteins.both.22Gv1.1.bestOrthos test-data/proteins.both.22Gv1.1.bestOrthos.summary test-data/proteins.hmmscan.22Gv1.1 test-data/proteins.hmmscan.22Gv1.1.bestOrthos test-data/transcripts.cleaned.nr.cds test-data/transcripts.cleaned.nr.pep tool_data_table_conf.xml.test
diffstat 14 files changed, 196 insertions(+), 71 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_classifier.xml	Tue May 30 08:13:52 2017 -0400
+++ b/gene_family_classifier.xml	Tue Jun 06 08:39:14 2017 -0400
@@ -82,8 +82,8 @@
                 #end if
             #end if
 
-            #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both' and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
-                --save_hmmscan_log
+            #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
+                --save_hmmscan_log 'true'
                 --hmmscan_log '$hmmscan_log'
             #end if
             #if $create_ortho_sequences:
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plant_tribes_scaffolds.loc	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,3 @@
+## Plant Tribes scaffolds
+#Value	Name	Path	Description
+22Gv1.1	22Gv1.1	${__HERE__}/test-data/tool-data/plant_tribes/scaffolds/22Gv1.1	22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- a/repository_dependencies.xml	Tue May 30 08:13:52 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="This tool uses the data installed by the data_manager_plant_tribes_scaffolds_downloader Data Manager tool.">
-    <repository changeset_revision="8bb32fd5b175" name="data_manager_plant_tribes_scaffolds_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.ptorthocs	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,28 @@
+<html><head><h3>Orthogroups and corresponding coding sequences files: 12 items</h3></head>
+<body><p/><table cellpadding="2">
+<tr><b>Datasets</th></b>
+<tr bgcolor="#D8D8D8"><td><a href="20.faa" type="text/plain">20.faa</a>
+</td></tr>
+<tr bgcolor="#FFFFFF"><td><a href="20.fna" type="text/plain">20.fna</a>
+</td></tr>
+<tr bgcolor="#D8D8D8"><td><a href="3494.faa" type="text/plain">3494.faa</a>
+</td></tr>
+<tr bgcolor="#FFFFFF"><td><a href="3494.fna" type="text/plain">3494.fna</a>
+</td></tr>
+<tr bgcolor="#D8D8D8"><td><a href="3722.faa" type="text/plain">3722.faa</a>
+</td></tr>
+<tr bgcolor="#FFFFFF"><td><a href="3722.fna" type="text/plain">3722.fna</a>
+</td></tr>
+<tr bgcolor="#D8D8D8"><td><a href="38889.faa" type="text/plain">38889.faa</a>
+</td></tr>
+<tr bgcolor="#FFFFFF"><td><a href="38889.fna" type="text/plain">38889.fna</a>
+</td></tr>
+<tr bgcolor="#D8D8D8"><td><a href="39614.faa" type="text/plain">39614.faa</a>
+</td></tr>
+<tr bgcolor="#FFFFFF"><td><a href="39614.fna" type="text/plain">39614.fna</a>
+</td></tr>
+<tr bgcolor="#D8D8D8"><td><a href="5235.faa" type="text/plain">5235.faa</a>
+</td></tr>
+<tr bgcolor="#FFFFFF"><td><a href="5235.fna" type="text/plain">5235.fna</a>
+</td></tr>
+</table></body></html>
--- a/test-data/proteins.blastp.22Gv1.1	Tue May 30 08:13:52 2017 -0400
+++ b/test-data/proteins.blastp.22Gv1.1	Tue Jun 06 08:39:14 2017 -0400
@@ -1,50 +1,50 @@
-contig_1	gnl|Soltu3.4|PGSC0003DMP400044471	92.11	114	9	0	1	114	15	128	9e-73	228
-contig_1	gnl|Mimgu1.0|PACid:17670850	92.98	114	8	0	1	114	307	420	1e-71	232
-contig_1	gnl|Soltu3.4|PGSC0003DMP400044470	92.11	114	9	0	1	114	313	426	6e-71	230
-contig_1	gnl|Soltu3.4|PGSC0003DMP400044472	92.11	114	9	0	1	114	313	426	6e-71	230
-contig_1	gnl|Solly2.3|Solyc04g083010.2.1	92.11	114	9	0	1	114	313	426	8e-71	230
-contig_1	gnl|Poptr2.2|PACid:18246737	91.23	114	10	0	1	114	301	414	3e-70	228
-contig_1	gnl|Nelnu1.0|NNU_016098-RA	90.35	114	11	0	1	114	315	428	3e-70	228
-contig_1	gnl|Carpa1.181|PACid:16417175	90.35	114	11	0	1	114	289	402	9e-70	227
-contig_1	gnl|Glyma1.01|PACid:16244092	90.35	114	11	0	1	114	298	411	1e-69	227
-contig_1	gnl|Glyma1.01|PACid:16244091	90.35	114	11	0	1	114	298	411	1e-69	227
-contig_1	gnl|Vitvi12X|PACid:17826505	90.35	114	11	0	1	114	229	342	1e-69	225
-contig_1	gnl|Theca1.0|Tc10_g016990	90.35	114	11	0	1	114	288	401	4e-69	225
-contig_1	gnl|Phoda3.0|PDK_30s1127391g001	88.60	114	13	0	1	114	146	259	8e-69	221
-contig_1	gnl|Glyma1.01|PACid:16251026	87.72	114	14	0	1	114	127	240	8e-69	220
-contig_1	gnl|Thepa2.0|Tp5g34670	89.47	114	12	0	1	114	310	423	1e-68	224
-contig_1	gnl|Orysa6.0|PACid:16860403	86.84	114	15	0	1	114	325	438	4e-68	219
-contig_1	gnl|Aquco1.0|PACid:18145344	88.60	114	13	0	1	114	320	433	8e-68	222
-contig_1	gnl|Orysa6.0|PACid:16860404	86.84	114	15	0	1	114	325	438	9e-68	222
-contig_1	gnl|Arath10|AT1G79600.1	89.47	114	12	0	1	114	308	421	1e-67	222
-contig_1	gnl|Bradi1.2|Bradi2g30567.2	88.60	114	13	0	1	114	300	413	1e-67	221
-contig_1	gnl|Sorbi1.4|PACid:1980340	85.96	114	16	0	1	114	312	425	3e-67	220
-contig_1	gnl|Glyma1.01|PACid:16251025	87.72	114	14	0	1	114	361	474	3e-67	221
-contig_1	gnl|Medtr3.5|Medtr4g026450.1	85.96	114	16	0	1	114	313	426	4e-67	220
-contig_1	gnl|Glyma1.01|PACid:16245030	86.84	114	15	0	1	114	326	439	7e-67	219
-contig_1	gnl|Glyma1.01|PACid:16245029	86.84	114	15	0	1	114	326	439	8e-67	219
-contig_1	gnl|Ambtr1.0.27|AmTr_v1.0_scaffold00022.11	85.09	114	17	0	1	114	310	423	4e-66	218
-contig_1	gnl|Frave2.0|gene29299	89.47	114	12	0	1	114	711	824	1e-65	219
-contig_1	gnl|Musac1.0|GSMUA_Achr10T01800_001	82.46	114	20	0	1	114	229	342	3e-65	214
-contig_1	gnl|Musac1.0|GSMUA_Achr8T21380_001	81.58	114	21	0	1	114	229	342	4e-64	208
-contig_1	gnl|Phypa1.6|PACid:18072969	81.58	114	21	0	1	114	498	611	8e-62	207
-contig_1	gnl|Selmo1.0|PACid:15405864	77.88	113	25	0	2	114	228	340	3e-58	195
-contig_1	gnl|Poptr2.2|PACid:18214805	54.31	116	49	2	3	114	279	394	1e-35	133
-contig_1	gnl|Selmo1.0|PACid:15417058	53.98	113	52	0	2	114	208	320	2e-35	132
-contig_1	gnl|Glyma1.01|PACid:16255045	51.89	106	51	0	9	114	308	413	6e-35	131
-contig_1	gnl|Vitvi12X|PACid:17841082	51.35	111	54	0	4	114	337	447	7e-35	131
-contig_1	gnl|Aquco1.0|PACid:18159073	53.15	111	51	1	5	114	165	275	1e-34	129
-contig_1	gnl|Nelnu1.0|NNU_020249-RA	53.33	105	49	0	10	114	45	149	1e-34	128
-contig_1	gnl|Solly2.3|Solyc08g068920.2.1	53.33	105	49	0	10	114	323	427	2e-34	130
-contig_1	gnl|Medtr3.5|Medtr3g105760.1	51.40	107	52	0	8	114	309	415	3e-34	129
-contig_1	gnl|Ambtr1.0.27|AmTr_v1.0_scaffold00019.389	54.29	105	48	0	10	114	330	434	4e-34	129
-contig_1	gnl|Phypa1.6|PACid:18069401	50.00	116	56	1	1	114	331	446	6e-34	129
-contig_1	gnl|Arath10|AT5G24970.2	50.47	107	53	0	8	114	363	469	1e-33	127
-contig_1	gnl|Thepa2.0|Tp2g22500	51.40	107	52	0	8	114	326	432	2e-33	127
-contig_1	gnl|Aquco1.0|PACid:18141086	53.51	114	45	1	1	114	17	122	2e-33	125
-contig_1	gnl|Mimgu1.0|PACid:17681633	52.38	105	50	0	10	114	191	295	2e-33	126
-contig_1	gnl|Musac1.0|GSMUA_Achr1T23540_001	50.93	108	53	0	7	114	313	420	3e-33	127
-contig_1	gnl|Phypa1.6|PACid:18063964	52.63	114	46	1	1	114	312	417	3e-33	127
-contig_1	gnl|Ambtr1.0.27|AmTr_v1.0_scaffold00010.332	51.75	114	47	1	1	114	293	398	4e-33	126
-contig_1	gnl|Phypa1.6|PACid:18051230	52.63	114	46	1	1	114	312	417	7e-33	126
-contig_1	gnl|Musac1.0|GSMUA_Achr4T09960_001	50.00	114	49	1	1	114	262	367	8e-33	125
+contig_1	gnl|Soltu3.4|PGSC0003DMP400044471	92.17	115	9	0	2	116	15	129	1e-73	231
+contig_1	gnl|Mimgu1.0|PACid:17670850	93.04	115	8	0	2	116	307	421	3e-72	234
+contig_1	gnl|Soltu3.4|PGSC0003DMP400044470	92.17	115	9	0	2	116	313	427	1e-71	233
+contig_1	gnl|Soltu3.4|PGSC0003DMP400044472	92.17	115	9	0	2	116	313	427	1e-71	233
+contig_1	gnl|Solly2.3|Solyc04g083010.2.1	92.17	115	9	0	2	116	313	427	1e-71	232
+contig_1	gnl|Nelnu1.0|NNU_016098-RA	90.43	115	11	0	2	116	315	429	5e-71	230
+contig_1	gnl|Poptr2.2|PACid:18246737	91.30	115	10	0	2	116	301	415	6e-71	230
+contig_1	gnl|Glyma1.01|PACid:16244092	90.43	115	11	0	2	116	298	412	2e-70	229
+contig_1	gnl|Glyma1.01|PACid:16244091	90.43	115	11	0	2	116	298	412	2e-70	229
+contig_1	gnl|Carpa1.181|PACid:16417175	90.43	115	11	0	2	116	289	403	2e-70	229
+contig_1	gnl|Vitvi12X|PACid:17826505	90.43	115	11	0	2	116	229	343	2e-70	228
+contig_1	gnl|Theca1.0|Tc10_g016990	90.43	115	11	0	2	116	288	402	7e-70	227
+contig_1	gnl|Phoda3.0|PDK_30s1127391g001	88.70	115	13	0	2	116	146	260	1e-69	224
+contig_1	gnl|Glyma1.01|PACid:16251026	87.83	115	14	0	2	116	127	241	1e-69	223
+contig_1	gnl|Orysa6.0|PACid:16860403	86.96	115	15	0	2	116	325	439	6e-69	221
+contig_1	gnl|Thepa2.0|Tp5g34670	89.57	115	12	0	2	116	310	424	1e-68	224
+contig_1	gnl|Aquco1.0|PACid:18145344	88.70	115	13	0	2	116	320	434	1e-68	224
+contig_1	gnl|Bradi1.2|Bradi2g30567.2	88.70	115	13	0	2	116	300	414	1e-68	224
+contig_1	gnl|Arath10|AT1G79600.1	89.57	115	12	0	2	116	308	422	2e-68	224
+contig_1	gnl|Glyma1.01|PACid:16251025	87.83	115	14	0	2	116	361	475	6e-68	223
+contig_1	gnl|Medtr3.5|Medtr4g026450.1	86.09	115	16	0	2	116	313	427	6e-68	223
+contig_1	gnl|Glyma1.01|PACid:16245030	86.96	115	15	0	2	116	326	440	1e-67	222
+contig_1	gnl|Glyma1.01|PACid:16245029	86.96	115	15	0	2	116	326	440	1e-67	222
+contig_1	gnl|Orysa6.0|PACid:16860404	86.96	115	15	0	2	116	325	439	2e-67	221
+contig_1	gnl|Sorbi1.4|PACid:1980340	86.09	115	16	0	2	116	312	426	2e-67	221
+contig_1	gnl|Ambtr1.0.27|AmTr_v1.0_scaffold00022.11	85.22	115	17	0	2	116	310	424	7e-67	219
+contig_1	gnl|Frave2.0|gene29299	89.57	115	12	0	2	116	711	825	2e-66	221
+contig_1	gnl|Musac1.0|GSMUA_Achr10T01800_001	82.61	115	20	0	2	116	229	343	4e-66	216
+contig_1	gnl|Musac1.0|GSMUA_Achr8T21380_001	81.74	115	21	0	2	116	229	343	6e-65	210
+contig_1	gnl|Phypa1.6|PACid:18072969	81.74	115	21	0	2	116	498	612	1e-62	209
+contig_1	gnl|Selmo1.0|PACid:15405864	78.07	114	25	0	3	116	228	341	4e-59	197
+contig_1	gnl|Poptr2.2|PACid:18214805	54.70	117	49	2	4	116	279	395	3e-36	135
+contig_1	gnl|Selmo1.0|PACid:15417058	56.60	106	46	0	11	116	216	321	3e-36	134
+contig_1	gnl|Glyma1.01|PACid:16255045	51.85	108	52	0	9	116	307	414	9e-36	134
+contig_1	gnl|Vitvi12X|PACid:17841082	51.79	112	54	0	5	116	337	448	1e-35	134
+contig_1	gnl|Aquco1.0|PACid:18159073	53.57	112	51	1	6	116	165	276	2e-35	131
+contig_1	gnl|Nelnu1.0|NNU_020249-RA	53.77	106	49	0	11	116	45	150	3e-35	130
+contig_1	gnl|Solly2.3|Solyc08g068920.2.1	53.77	106	49	0	11	116	323	428	5e-35	132
+contig_1	gnl|Medtr3.5|Medtr3g105760.1	51.85	108	52	0	9	116	309	416	5e-35	132
+contig_1	gnl|Phypa1.6|PACid:18069401	50.43	117	56	1	2	116	331	447	1e-34	131
+contig_1	gnl|Aquco1.0|PACid:18141086	53.91	115	45	1	2	116	17	123	3e-34	127
+contig_1	gnl|Arath10|AT5G24970.2	50.93	108	53	0	9	116	363	470	3e-34	130
+contig_1	gnl|Thepa2.0|Tp2g22500	51.85	108	52	0	9	116	326	433	3e-34	129
+contig_1	gnl|Mimgu1.0|PACid:17681633	52.83	106	50	0	11	116	191	296	3e-34	128
+contig_1	gnl|Ambtr1.0.27|AmTr_v1.0_scaffold00019.389	54.29	105	48	0	11	115	330	434	4e-34	129
+contig_1	gnl|Musac1.0|GSMUA_Achr1T23540_001	51.38	109	53	0	8	116	313	421	5e-34	129
+contig_1	gnl|Phypa1.6|PACid:18063964	53.04	115	46	1	2	116	312	418	6e-34	129
+contig_1	gnl|Phypa1.6|PACid:18051230	53.04	115	46	1	2	116	312	418	1e-33	128
+contig_1	gnl|Bradi1.2|Bradi1g28540.1	47.75	111	58	0	6	116	299	409	2e-33	127
+contig_1	gnl|Theca1.0|Tc09_g001090	53.77	106	49	0	11	116	332	437	2e-33	127
--- a/test-data/proteins.blastp.22Gv1.1.bestOrthos	Tue May 30 08:13:52 2017 -0400
+++ b/test-data/proteins.blastp.22Gv1.1.bestOrthos	Tue Jun 06 08:39:14 2017 -0400
@@ -1,5 +1,7 @@
 Gene ID	Orthogroup ID
+contig_10	3494
+contig_7	3722
 contig_3	554
+contig_2	38889
 contig_1	5235
-contig_2	38889
 contig_9	20
--- a/test-data/proteins.blastp.22Gv1.1.bestOrthos.summary	Tue May 30 08:13:52 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-Gene ID	Orthogroup ID	Arabidopsis thaliana	Thellungiella parvula	Carica papaya	Theobroma cacao	Populus trichocarpa	Fragaria vesca	Glycine max	Medicago truncatula	Vitis vinifera	Solanum lycopersicum	Solanum tuberosum	Mimulus guttatus	Nelumbo nucifera	Aquilegia coerulea	Oryza sativa	Brachypodium distachyon	Sorghum bicolor	Musa acuminata	Phoenix dactylifera	Amborella trichopoda	Selaginella moellendorffii	Physcomitrella patens	SuperOthogroup I1.2	SuperOthogroup I1.5	SuperOthogroup I1.8	SuperOthogroup I2.0	SuperOthogroup I2.5	SuperOthogroup I3.0	SuperOthogroup I3.5	SuperOthogroup I4.0	SuperOthogroup I4.5	SuperOthogroup I5.0	AHRD Descriptions	TAIR Gene(s) Descriptions	Pfam Domains	InterProScan Descriptions	GO Molecular Functions	GO Biological Processes	GO Cellular Components
-contig_3	554	4	4	3	3	8	3	9	2	3	6	8	4	5	3	4	4	5	6	5	3	1	4	53	40	37	35	3078	3326	3484	3611	3699	3800	P-loop containing nucleoside triphosphate hydrolases superfamily protein [0.557] | Kinesin-related protein 13 [0.423] | kinesin 4 [0.010] | kinesin 5 [0.010]	P-loop containing nucleoside triphosphate hydrolases superfamily protein | ATP binding microtubule motor family protein	Kinesin (PF00225) [0.979]	Kinesin, motor domain (IPR001752) [0.979]	ATP binding (GO:0005524) [0.979] | microtubule binding (GO:0008017) [0.979] | microtubule motor activity (GO:0003777) [0.979]	microtubule-based movement (GO:0007018) [0.979]	NULL / Representative annotation below 0.1%
-contig_1	5235	1	1	1	1	1	1	6	1	1	1	3	1	1	1	2	1	1	2	1	1	1	1	2	207	198	330	347	338	461	452	558	557	Protein kinase superfamily protein [1.000]	Protein kinase superfamily protein	ABC1 (PF03109) [0.968] | APH (PF01636) [0.161]	UbiB domain (IPR004147) [0.968] | Aminoglycoside phosphotransferase (IPR002575) [0.161]	NULL / Representative annotation below 0.1%	NULL / Representative annotation below 0.1%	NULL / Representative annotation below 0.1%
-contig_2	38889	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	489	741	746	752	773	800	798	1128	1403	1407	6-phosphogluconolactonase 5 [0.500] | 6-phosphogluconolactonase 2 [0.500]	Unkown protein(s) / No TAIR description(s)	Glucosamine_iso (PF01182) [1.000]	Glucosamine/galactosamine-6-phosphate isomerase (IPR006148) [1.000]	NULL / Representative annotation below 0.1%	carbohydrate metabolic process (GO:0005975) [1.000]	NULL / Representative annotation below 0.1%
-contig_9	20	3	35	0	3	15	7	16	70	0	25	5	1	0	339	4	9	44	0	0	0	3	2	2	21	26	25	23	30	28	29	29	29	ATP-dependent DNA helicase PIF1 [0.435] | PIF1 helicase [0.138] | ATP-dependent DNA helicase pif1 [0.138] | ATP-dependent DNA helicase RRM3 [0.014] | ATP-dependent DNA helicase PIF4 [0.014] | F-box/RNI-like/FBD-like domains-containing protein [0.003] | ATP-dependent DNA helicase pfh1 [0.002] | Protein kinase superfamily protein [0.002] | Nucleic acid-binding, OB-fold-like protein [0.002] | Phosphatidylinositol N-acetylglucosaminyltransferase, GPI19/PIG-P subunit [0.002] | ATP-dependent DNA helicase PIF2 [0.002]	PIF1 helicase	PIF1 (PF05970) [0.771] | Helitron_like_N (PF14214) [0.503] | Herpes_Helicase (PF02689) [0.349] | Rep_fac-A_C (PF08646) [0.009] | DUF223 (PF02721) [0.009] | ABC1 (PF03109) [0.003] | Phage_GPA (PF05840) [0.002] | AAA_30 (PF13604) [0.002]	DNA helicase Pif1 like (IPR010285) [0.771] | Helitron helicase-like domain (IPR025476) [0.503] | DNA helicase (IPR003840) [0.349] | Replication factor A, C-terminal (IPR013955) [0.009] | Domain of unknown function DUF223 (IPR003871) [0.009] | UbiB domain (IPR004147) [0.003] | Replication gene A protein (IPR008766) [0.002]	DNA helicase activity (GO:0003678) [0.771] | ATP binding (GO:0005524) [0.349] | helicase activity (GO:0004386) [0.349]	telomere maintenance (GO:0000723) [0.771] | DNA repair (GO:0006281) [0.771] | DNA replication (GO:0006260) [0.002]	NULL / Representative annotation below 0.1%
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteins.both.22Gv1.1.bestOrthos	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,7 @@
+Gene ID	Orthogroup ID
+contig_1	5235
+contig_10	3494
+contig_2	38889
+contig_3	39614
+contig_7	3722
+contig_9	20
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteins.both.22Gv1.1.bestOrthos.summary	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,4 @@
+Gene ID	Orthogroup ID	Arabidopsis thaliana	Thellungiella parvula	Carica papaya	Theobroma cacao	Populus trichocarpa	Fragaria vesca	Glycine max	Medicago truncatula	Vitis vinifera	Solanum lycopersicum	Solanum tuberosum	Mimulus guttatus	Nelumbo nucifera	Aquilegia coerulea	Oryza sativa	Brachypodium distachyon	Sorghum bicolor	Musa acuminata	Phoenix dactylifera	Amborella trichopoda	Selaginella moellendorffii	Physcomitrella patens	SuperOthogroup I1.2	SuperOthogroup I1.5	SuperOthogroup I1.8	SuperOthogroup I2.0	SuperOthogroup I2.5	SuperOthogroup I3.0	SuperOthogroup I3.5	SuperOthogroup I4.0	SuperOthogroup I4.5	SuperOthogroup I5.0	AHRD Descriptions	TAIR Gene(s) Descriptions	Pfam Domains	InterProScan Descriptions	GO Molecular Functions	GO Biological Processes	GO Cellular Components
+contig_1	5235	1	1	1	1	1	1	6	1	1	1	3	1	1	1	2	1	1	2	1	1	1	1	2	207	198	330	347	338	461	452	558	557	Protein kinase superfamily protein [1.000]	Protein kinase superfamily protein	ABC1 (PF03109) [0.968] | APH (PF01636) [0.161]	UbiB domain (IPR004147) [0.968] | Aminoglycoside phosphotransferase (IPR002575) [0.161]	NULL / Representative annotation below 0.1%	NULL / Representative annotation below 0.1%	NULL / Representative annotation below 0.1%
+contig_10	3494	1	1	1	1	3	1	4	1	0	1	1	1	3	1	3	5	3	3	4	1	0	0	96	177	236	239	529	538	532	524	780	779	RING/U-box superfamily protein [1.000]	RING/U-box superfamily protein	zf-C3HC4_2 (PF13923) [0.949] | zf-RING_5 (PF14634) [0.026]	Zinc finger, RING-type (IPR001841) [0.026]	protein binding (GO:0005515) [0.026] | zinc ion binding (GO:0008270) [0.026]	NULL / Representative annotation below 0.1%	NULL / Representative annotation below 0.1%
+contig_2	38889	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	489	741	746	752	773	800	798	1128	1403	1407	6-phosphogluconolactonase 5 [0.500] | 6-phosphogluconolactonase 2 [0.500]	Unkown protein(s) / No TAIR description(s)	Glucosamine_iso (PF01182) [1.000]	Glucosamine/galactosamine-6-phosphate isomerase (IPR006148) [1.000]	NULL / Representative annotation below 0.1%	carbohydrate metabolic process (GO:0005975) [1.000]	NULL / Representative annotation below 0.1%
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteins.hmmscan.22Gv1.1	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,25 @@
+#                                                               --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
+# target name        accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
+#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
+5235                 -          contig_1             -            9.1e-80  270.0   0.0   9.9e-80  269.9   0.0   1.0   1   0   0   1   1   1   1 -
+10465                -          contig_1             -              5e-45  155.1   0.0   5.8e-45  154.9   0.0   1.0   1   0   0   1   1   1   1 -
+9351                 -          contig_1             -            4.7e-41  142.1   0.0   5.2e-41  142.0   0.0   1.0   1   0   0   1   1   1   1 -
+20322                -          contig_1             -              2e-35  123.0   0.0   2.3e-35  122.8   0.0   1.0   1   0   0   1   1   1   1 -
+7049                 -          contig_1             -            3.9e-29  102.4   0.0   4.4e-29  102.3   0.0   1.0   1   0   0   1   1   1   1 -
+5553                 -          contig_1             -            8.8e-29  101.7   0.0     1e-28  101.4   0.0   1.0   1   0   0   1   1   1   1 -
+2922                 -          contig_1             -            7.3e-28   97.8   0.0   8.5e-28   97.6   0.0   1.0   1   0   0   1   1   1   1 -
+8140                 -          contig_1             -              5e-26   92.3   0.2   1.6e-24   87.3   0.2   2.0   1   1   0   1   1   1   1 -
+4060                 -          contig_1             -            1.6e-22   80.8   0.0   1.9e-22   80.6   0.0   1.0   1   0   0   1   1   1   1 -
+8330                 -          contig_1             -            3.7e-17   63.4   0.0   4.2e-17   63.2   0.0   1.0   1   0   0   1   1   1   1 -
+3825                 -          contig_1             -            4.3e-13   50.4   0.0     7e-13   49.7   0.0   1.3   1   1   0   1   1   1   1 -
+4099                 -          contig_1             -            9.7e-13   48.1   0.0   1.1e-12   47.8   0.0   1.0   1   0   0   1   1   1   1 -
+10051                -          contig_1             -            1.1e-10   42.0   0.0   1.4e-10   41.7   0.0   1.0   1   0   0   1   1   1   1 -
+8737                 -          contig_1             -            1.3e-10   41.9   0.0   1.6e-10   41.7   0.0   1.0   1   0   0   1   1   1   1 -
+25529                -          contig_1             -            2.1e-08   34.3   0.0   2.6e-08   34.0   0.0   1.0   1   0   0   1   1   1   1 -
+40021                -          contig_1             -            6.1e-08   32.9   0.0   6.7e-08   32.8   0.0   1.0   1   0   0   1   1   1   1 -
+3494                 -          contig_10            -              1e-06   28.1   0.1   1.1e-06   28.0   0.1   1.0   1   0   0   1   1   1   1 -
+38889                -          contig_2             -            1.1e-87  295.2   0.2   1.4e-87  294.9   0.2   1.0   1   0   0   1   1   1   1 -
+3534                 -          contig_2             -            1.6e-72  245.8   0.1   1.8e-72  245.7   0.1   1.0   1   0   0   1   1   1   1 -
+4875                 -          contig_2             -            1.1e-62  213.8   0.0   1.3e-62  213.6   0.0   1.0   1   0   0   1   1   1   1 -
+37475                -          contig_2             -            6.1e-49  168.3   0.0   7.1e-49  168.1   0.0   1.0   1   0   0   1   1   1   1 -
+28488                -          contig_2             -            1.1e-45  157.4   0.0   1.4e-45  157.0   0.0   1.0   1   0   0   1   1   1   1 -
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteins.hmmscan.22Gv1.1.bestOrthos	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,7 @@
+Gene ID	Orthogroup ID
+contig_9	20
+contig_1	5235
+contig_2	38889
+contig_10	3494
+contig_7	3722
+contig_3	39614
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcripts.cleaned.nr.cds	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,43 @@
+>contig_1
+NTTAAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAAC
+AATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGA
+ATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTA
+GCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAAT
+TGGTCATGTTGTACACATGGTTAATCGN
+>contig_10
+ATGGCAGAAGAGAACACCACTACAATGAACCTCGATCTCAATTTGGGCCCCATCAATAACTCAAGCGACGATAGCGAACC
+TTCATCACGCCCTTATACTGATGTCGCAATGAACTTGGAAGATTGGTTAGATAGTCCCGTCCGAGTTCGTGAAGTCGTCC
+GCCACAGAAATCATAGGTGGCGCTCTTTGTGGCGCCAAATCCCAATTCCGCCTGATACGCGAAACCTCGCGCTCGAATTA
+ATCGGCGGCAATGCCCCN
+>contig_2
+NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA
+CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC
+TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA
+TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC
+GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC
+CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA
+CAACTGTTAAATTATGTGCGCTTTGATGAT
+>contig_3
+NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG
+AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA
+CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC
+ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT
+TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC
+>contig_5
+NNCGGTGGTCCGCCACAAACACACGTCAAGCGGGATCCCGCATCCCGCGGGCTCTTCCACGCGGTCGTCCCGGCGCTCGG
+CCCTCTCCGTGACGCACGTCGAGAGGGACGATTTGGCCGATGCCGCGTGATGCCAGGCCCCGACATCATCAAGGAGCACT
+CCGTTGTGCCGACCCTCGCCTTCGATGACGTCCTCGGGCGTCTAGCGAAGTATCGAAGAAGGGCGAGCGGAGCCATGAAT
+CCTGGAGATGCGAGCCAGGTCACGAGAGGCGCGGCAGGCGAGTCTTTGCTCGCTCTCGCACCGTCTGCTCTCGTGCTTGG
+AGAAGAAGGACCGACTGCTGACGTCGAACCGGATGATGGAAGGTTCGAACAAGTCAGATCTGGAAAGGGGCATGGAAAAG
+GCGACACTCTCACN
+>contig_7
+GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC
+CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT
+CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA
+AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN
+>contig_9
+NNACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCA
+TGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCT
+CAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGA
+ACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGC
+TGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGAN
--- a/test-data/transcripts.cleaned.nr.pep	Tue May 30 08:13:52 2017 -0400
+++ b/test-data/transcripts.cleaned.nr.pep	Tue Jun 06 08:39:14 2017 -0400
@@ -1,13 +1,22 @@
 >contig_1
-KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA
-TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN
+XKKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLL
+ATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVNR
+>contig_10
+MAEENTTTMNLDLNLGPINNSSDDSEPSSRPYTDVAMNLEDWLDSPVRVREVVRHRNHRWRSLWRQIPIPPDTRNLALEL
+IGGNAP
 >contig_2
-LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW
-VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ
-LLNYVRFDD
+XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK
+WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS
+QLLNYVRFDD
 >contig_3
-VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGT
-IESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN
+XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG
+TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN
+>contig_5
+XGGPPQTHVKRDPASRGLFHAVVPALGPLRDARREGRFGRCRVMPGPDIIKEHSVVPTLAFDDVLGRLAKYRRRASGAMN
+PGDASQVTRGAAGESLLALAPSALVLGEEGPTADVEPDDGRFEQVRSGKGHGKGDTLT
+>contig_7
+ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG
+NESGEISGKKNTRKGKGDX
 >contig_9
-LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT
-AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
+XLRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGR
+TAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAVX
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Jun 06 08:39:14 2017 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="plant_tribes_scaffolds" comment_char="#">
+        <columns>value, name, path, description</columns>
+        <file path="${__HERE__}/plant_tribes_scaffolds.loc" />
+    </table>
+</tables>