Repository 'geneseqtofamily'
hg clone https://toolshed.g2.bx.psu.edu/repos/earlhaminst/geneseqtofamily

Changeset 2:58c9294400ed (2017-05-12)
Previous changeset 1:267a94f068d7 (2017-02-20) Next changeset 3:fd620c523d63 (2017-05-18)
Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit d3da4ff3bfb86ce0686a87c4987e94486854d839
modified:
GeneSeqToFamily.ga
test-data/CDS.fasta
added:
test-data/gene.json
test-data/gene_family.gafa.sqlite
test-data/species.nhx
removed:
test-data/gene_feature.json
test-data/species_tree.nhx
b
diff -r 267a94f068d7 -r 58c9294400ed GeneSeqToFamily.ga
--- a/GeneSeqToFamily.ga Mon Feb 20 12:57:16 2017 -0500
+++ b/GeneSeqToFamily.ga Fri May 12 11:50:14 2017 -0400
[
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b
diff -r 267a94f068d7 -r 58c9294400ed test-data/CDS.fasta
--- a/test-data/CDS.fasta Mon Feb 20 12:57:16 2017 -0500
+++ b/test-data/CDS.fasta Fri May 12 11:50:14 2017 -0400
b
b'@@ -1,468 +1,1266 @@\n->ENSFCAT00000013089_feliscatus\n-ATGGCGAGTCGGGAGAAGGCGAGTGTCGCGGGCCACATGTTCGACGTAGTCGTGATAGGAGGCGGCATCTCAGGGCTGTCTGCCGCCAAACTCTTAGCTGAACATGAAGTGAATGTTTTGGTCTTAGAAGCGCGGGACAGAGTTGGAGGAAGAACATACACTGTGAGGAATGAACACGTCAATTACGTAGATGTTGGCGGGGCATATGTGGGACCAACCCAGAATAGAATCTTACGGTTATCTAAGGAGCTGGGTCTAGAAACTTACAAAGTGAACGTATGTGAGCGGCTTGTTCAATATGTAAAGGGGAAAACTTATCCTTTTCGGGGCGCCTTTCCTCCGGTGTGGAATCCTGTCGCGTATTTGGATTACAACAATCTGTGGCGGACAATGGATAACATGGGGAAGGAGATTCCAGCCGATGCACCATGGGAGGCCCCACATGCTAAGGAATGGGACAAGATGACCATGAAAGAGCTCATCGATAAAATCTGCTGGACAAAGACTGCTAGGCAATTTGCATATCTCTTCGTGAACATCAATGTGACCTCTGAACCCCACGAGGTGTCTGCGCTGTGGTTCCTGTGGTACGTGAAACAGTGTGGAGGCACCACTCGGATATTCTCGGTTACCAATGGGGGCCAGGAACGGAAGTTTGTGGGTGGATCTGGTCAAGTGAGCGAACGGATAATGGACCGCCTCGGGGACAGGGTGAAGCTGAAGCGTCCTGTCACCTATGTTGACCAGTCAGGTGACAGCATCATCATAGAGACGTTGAATCATGAAGTGTATGAGTGCAGATACGTAATTAGCGCCATCCCTCCAACATTGACTGCCAAGATGCACTTCAAACCAGAGCTTCCGTCAGAGAGAAACCAGTTAATTCAACGTCTTCCGATGGGATCTATCATTAAGTGCATGATGTATTACAAGGAGGCCTTTTGGAAGAAGAACGATTATTGTGGCTGTATGATCATTCAAGATGAGGAAGCACCCATCTCAATAACTCTGGATGACACCAAGCCAGATGGATCACTGCCTGCTATCATGGGATTCATACTTGCCCGAAAAGCAGACCGACTTGCCAAGCTCCATAAAGAAATCAGGAAGAAGAAAATCTGTGAGCTGTACGCCAAAGTGCTAGGATCCCAAGAAGCTTTACACCCCGTGCACTATGAAGAGAAGAACTGGTGCGAGGAGCAATACTCTGGGGGCTGTTACACCGCCTACTTCCCCCCTGGGATCATGACTCAATATGGAAGGGTGATCCGCCAGCCGGTCGGCAGGATTTACTTTGCGGGCACTGAGACTGCCACACACTGGAGCGGTTACATGGAAGGGGCAGTAGAGGCTGGAGAGAGAGCTGCTAGAGAGGTCTTGAATGCTCTCGGGAAGGTGGCGAAGAAGGACATCAAGGTTCAAGAACCTGAATCAAAGGACGTTCCAGCTGTAGAGATCACCCGCACCTTTTGGGAGAGAAACCTTCCCTCAGTGTCAGGACTGCTGAAGATCATCGGATTTACCACCTCAGTAACTGCCGTGTGGATTGTGGTGCACAAATTCAGGCTCCTGTCCCGGTCATGA\n-\n->ENSCAFT00000022939_canisfamiliaris\n-ATGGCGAGTAGAGAGAAGACGAGTATCGAGGGCCACATGTTTGACGTAGTCGTGATAGGAGGCGGCATCTCAGGATTGTCTGCTGCCAAACTCTTAGCCGAACATGAAGTTGATGTCTTAGTTTTAGAAGCACGAGATAGAGTTGGAGGAAGAACATACACCGTGAGGAATGAACATGTCGATTACGTAGATGTTGGTGGGGCTTATGTAGGACCAACTCAGAACAGAATCTTACGACTATCTAAGGAGCTGGGTCTAGAGACTTACAAAGTGAACGTAAATGAGCGTCTTGTACAGTATGTCAAGGGGAAAACTTACCCATTCCGAGGAGCCTTTCCTCCGGTATGGAATCCTATCGCATATTTGGATTACAACAACCTGTGGCGGACAATGGATAACATGGGGAAGGAGATTCCAGCAGATGCACCATGGGAGGCCCCACATGCCGAGGAATGGGACAAGATGACTATGAAGGATCTTATCGATAAAATCTGCTGGACAAAGACTGCTAGGAGGTTTGCATCCCTCTTTGTGAATATCAATGTGACCTCTGAGCCCCACGAGGTGTCTGCGCTCTGGTTCCTGTGGTATGTGAAGCAGTGCGGAGGTACCACTCGGATATTCTCGGTGACCAATGGAGGCCAGGAACGGAAGTTTGTGGGAGGATCCGGTCAAGTGAGTGAACGGATAATGGAGCGCCTTGGGGACAGAGTCAAGCTGAAGCGCCCTGTCACCTATGTTGACCAGTCAGATGACAACATCATCATAGAGACACTGAATCATGAACTTTATGAGTGCAAATACGTGATTAGTGCCATCCCTCCAACTTTGACTGCCAAGATCCACTTCAGACCAGAGCTTCCATCAGAGAGAAATCAGTTAATTCAGCGTCTTCCAATGGGAGCTATCATCAAGTGTATGATGTATTACAAGGAGGCCTTTTGGAAGAAGAAGGATTACTGTGGCTGTATGATCATTGAAGACGAGGAAGCTCCAATTTCAATAACCCTGGATGACACCAAGCCAGATGGATCACTGCCCGCTATCATGGGCTTCATACTTGCCAGAAAAGCTGACCGACTTGCCAAGCTCCATAAAGAAATAAGGAAGAGGAAAATCTGTGAGCTCTATGCCAAAGTGCTAGGATCCCAAGAAGCTTTACAACCCGTACACTATGAAGAGAAGAACTGGTGCGAGGAGCAGTACTCCGGGGGCTGCTATACCGCCTACTTCCCCCCTGGGATCATGACTCACTACGGAAGGGTGATCCGCCAGCCATTTGGCAGGATTTACTTTGCTGGCACTGAGACGGCAACACACTGGAGCGGTTATATGGAAGGAGCTGTAGAGGCTGGGGAACGGACAGCTAGAGAGGTCTTAAATGCTCTCGGGAGGGTGGCAGAGAAAGACCTGAAGACCCAGGAACCTGAATCAAAGGATGTTCCAGCTATGGAAATCACCCACACCTTCTGGGAGAGGAACCTGCCATCGGTGACAGGCCTGCTGAAGCTCATTGGATTTACCACATCAGTAACTGCCCTGTGGATTGTGGCGTACAAATTCAGGCTGCTGAGACGATCCTGA\n-\n->ENSAMXT00000002585_astyanaxmexicanus\n-ATGGCAGCCAACACGTACGATGTGATCGTGATCGGGGGAGGAATCTCAGGTCTGAGTGCAGCCAAGCTGTTGGTGGAGAGTGGTTTAAACCCTGTACTGCTGGAGGCCAGAGACCGAGTCGGTGGAAGAACCTTCACAGTTCAGAATAAACAGACCAAATGGGTGGACCTGGGCGGAGCTTATATCGGACCCACTCAAAACCGAATCCTGAGGTTGGCCAAGCAGTACGGGGTTCAGACCTACAAGGTGAATGAAGAGGAGTCGCTGGTTCACTATGTGAAGGGGAAATCATATCCATTCAAGGGGCCTTTCCCACTGATGTGGAACCCTCTAGCTCTGATGGACTACAACAACCTCTGGAGGACTATGGACAAGATGGGCATGGAGATCCCTAAAGAAGCTCCATGGAGAGCCCCACATGCTGAGGAGTGGGACAAGATGACCATGCATGAGTTCTTTGACAAGGTTTGCTGGACCAGCGCTGCCCGTCGCTTTGCCACGCTGTTCGTTAACGTGAACGTGACCTCAGAGCCTCATGAAGTGTCAGCTCTCTGGTTCCTCTGGTACGTCAAGCAGTGTGGAGGAACCATGAGGATCTTCTCCACCACTAATGGTGGCCAGGAGCGTAAGTTTGTTGGAGGCTCGAGTCAGATCAGCGAGTGCATGGCCAGAGAGCTGGGAGACCGGGTGAAG'..b'AAGCACAATCAG\n+AGTGAGTATGACGACTCGGCCAGCGAGTGCTGCTCATGTCCTAAGACTGACTCTCAGATC\n+CTGAAGGAGCTGGAGGAGTCTTCATTCAGGAAGACCTTCGAGGATTACCTGCACAACGTG\n+GTTTTTGTTCCCAGAAAAACCTCTTCAGGCAATGGTGCTGAGGACACTAGGCCATCCCGA\n+AAGCGAAGATCCCTTGAAGAGGTGGGCAATGTGACAGCCACTACACCCACACTTCCAGAT\n+TTTCCCAACATCTCCTCCACCATCGCGCCCACAAGCCACGAAGAGCACAGACCATTTGAG\n+AAAGTAGTAAACAAGGAGTCACTTGTCATCTCTGGCCTGAGACACTTCACTGGGTACCGC\n+ATTGAGCTGCAGGCATGCAATCAGGACTCCCCAGAAGAGAGGTGCAGCGTGGCTGCCTAC\n+GTCAGTGCCCGGACCATGCCTGAAGCTAAGGCAGATGACATCGTTGGCCCTGTGACCCAT\n+GAAATCTTTGAGAACAATGTTGTACACTTAATGTGGCAAGAGCCAAAGGAACCTAATGGT\n+CTGATTGTGCTATATGAAGTGAGCTATCGGCGATATGGTGATGAGGAGCTGCACCTCTGT\n+GTCTCCCGGAAGCATTTTGCCCTGGAGCGGGGCTGCAGGCTTCGAGGGCTCTCTCCAGGA\n+AACTACAGTGTTCGAGTCCGGGCTACCTCTCTGGCAGGAAATGGCTCCTGGACAGAACCC\n+ACCTATTTTTATGTGACTGATTATTTAGATGTCCCATCAAATATTGCCAAAATTATCATC\n+GGGCCCCTCATCTTCGTCTTCCTCTTCAGTGTCGTGATCGGAAGTATTTATCTATTCTTG\n+AGGAAGAGGCAGCCAGATGGGCCAATGGGACCACTGTACGCTTCTTCAAACCCAGAGTAC\n+CTCAGTGCCAGTGATGTCTTTCCATCTTCCGTATACGTTCCGGATGAGTGGGAGGTACCT\n+CGAGAGAAGATCACCCTCCTCCGAGAGCTGGGGCAGGGATCCTTCGGTATGGTGTACGAA\n+GGCAATGCCAAGGATATCATCAAGGGTGAGGTAGAGACCCGTGTTGCGGTGAAGACGGTC\n+AATGAGTCAGCCAGTCTTCGAGAACGGATCGAGTTCCTCAATGAGGCATCAGTCATGAAG\n+GGCTTCACCTGTCATCACGTGGTCCGCCTTCTTGGGGTGGTGTCCAAAGGCCAGCCCACA\n+TTGGTAGTGATGGAACTGATGGCTCATGGAGACCTGAAAAGTCACCTCCGTTCTCTGCGG\n+CCCGATGCTGAGAACAACCCAGGCCGTCCTCCCCCTACCTTGCAAGAAATGATTCAGATG\n+ACAGCAGAAATTGCCGATGGCATGGCATACTTGAACGCCAAGAAGTTTGTGCACCGGGAC\n+CTGGCAGCTCGGAACTGCATGGTTGCCCATGATTTTACTGTCAAAATCGGAGACTTTGGA\n+ATGACGAGAGACATCTACGAGACAGATTACTATCGGAAAGGGGGCAAGGGGTTGCTGCCC\n+GTGAGGTGGATGTCACCCGAGTCCCTGAAGGACGGAGTCTTCACTGCTTCTTCCGACATG\n+TGGTCCTTTGGGGTGGTCCTTTGGGAAATCACCAGCCTGGCTGAGCAACCTTACCAAGGC\n+CTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGCTATCTGGATCCCCCTGAT\n+AACTGTCCAGAGAGACTCACTGACCTGATGCGCATGTGCTGGCAGTTCAACCCCAAGATG\n+AGGCCGACCTTCCTGGAAATCGTCAACCTGCTCAAGGACGACCTCCACCCCAGCTTTCCG\n+GAAGTTTCCTTCTTCTACAGCGAGGAGAACAAGGCTCCCGAGAGTGAAGAGCTGGAGATG\n+GAGTTCGAGGACATGGAGAATGTCCCCTTGGATCGTTCCTCTCACTGTCAGAGAGAAGAG\n+GCTGGATGCCGGGAGGGAGGGTCCTCTCTGAGCATCAAACGGACCTATGATGAACACATC\n+CCCTACACCCACATGAACGGGGGCAAGAAGAATGGGCGGGTCCTCACCCTGCCGAGGTCG\n+AACCCTTCCTAA\n+>ENSSSCT00000014817_susscrofa\n+GTGTGCCCAGGGATGGATATCCGGAATAACCTTACACGGCTGCACGAGTTGGCCAACTGC\n+TCGGTCATCGAAGGACATTTGCAGATCCTGTTGATGTTCAAAACGCGGCCCGAGGATTTC\n+CGAGACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTC\n+TACGGGCTGGAGAGCCTGAAGGACCTGTTCCCCAACCTCACCGTCATCCGGGGCTCACGC\n+CTCTTCTTTAACTATGCGCTGGTCATCTTTGAGATGGTTCACTTGAAGGAGCTTGGCCTC\n+TACAATTTGATGAACATCACCAGGGGTGCTGTCCGCATCGAGAAGAACAATGAGCTCTGC\n+TACCTGGCGACCATTGACTGGTCGCGCATCCTGGACTCTGTGGAGGATAATTACATTGTG\n+CTGAACAAAGACGACAACGAGGAGTGTGGGGACATTTGCCCAGGCACTGCGAAGGGCAAG\n+ACCAATTGCCCTGCCACCGTCATCAATGGGCAATTTGTCGAGCGGTGTTGGACGCACAGT\n+CACTGCCAGAAAGTGTGCCCGACCATCTGTAAGTCGCACGGCTGCACTGCTGAGGGCCTC\n+TGCTGTCACAGCGAGTGTTTGGGCAACTGCTCTGAGCCAGACGACCCCACCAAGTGCGTG\n+GCCTGCCGCAACTTCTACCTGGACGGCAGATGCGTGGAGACCTGCCCGCCCCCCTACTAC\n+CACTTCCAAGACTGGCGCTGCGTGAACTTCAGCTTCTGCCAGGACCTGCACAACAAATGC\n+AAGAACTCAAGGAGGCAGGGCTGCCACCAGTACGTCATTCACAACAACAAGTGTATCCCT\n+GAGTGCCCCTCAGGGTACACGATGAATTCCAGCAACTTGATGTGCACTCCGTGCCTAGGC\n+CCCTGTCCCAAAGTGTGTCACCTCCTGGAAGGCGAGAAGACCATCGACTCAGTGACATCC\n+GCCCAGGAGCTCCGAGGCTGCACCATTATCAACGGGAGCCTAATCATCAACATTCGAGGA\n+GGCAACAACCTGGCAGCCGAACTAGAGGCCAACCTTGGACTCATTGAGGAGATTTCAGGG\n+TACCTGAAAATCCGCCGATCCTATGCCCTCGTGTCACTTTCCTTCTTCCGGAAGTTGCGT\n+CTGATCCGAGGGGAGACGTTGGAAATTGGGAACTATTCTTTCTATGCCTTGGACAACCAG\n+AACCTAAGGCAACTGTGGGACTGGAGCAAACACAACCTCACCATCACTCAGGGGAAACTC\n+TTCTTCCATTATAATCCCAAACTCTGCTTGTCGGAAATTCACAAGATGGAGGAAGTTTCT\n+GGAACCAAGGGGCGCCAGGAGAGAAATGATATTGCCCTGAAGACCAATGGGGACCAGGCG\n+TCCTGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTATGACAAGATCTTG\n+CTGAAGTGGGAGCCGTATTGGCCCCCCGACTTCCGAGACCTCCTGGGGTTCATGCTCTTC\n+TACAAAGAGGCCCCTTATCAGAACGTGACGGAGTTTGACGGGCAGGATGCGTGTGGCTCC\n+AACAGCTGGACGGTGGTGGACATTGACCCGCCTACGAGGTCCAATGACCCCAAGTCCCAG\n+AACCATCCTGGGTGGCTGATGCGTGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTC\n+AAGACTTTGGTCACCTTTTCTGATGAACGACGCACCTATGGAGCCAAGAGTGACATCATC\n+TACGTCCAGACAGATGCCACAAGTAAGCATGTC\n'
b
diff -r 267a94f068d7 -r 58c9294400ed test-data/gene.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene.json Fri May 12 11:50:14 2017 -0400
[
b'@@ -0,0 +1,9586 @@\n+{\n+   "ENSG00000171105": {\n+      "assembly_name": "GRCh38", \n+      "display_name": "INSR", \n+      "description": "insulin receptor [Source:HGNC Symbol;Acc:HGNC:6091]", \n+      "seq_region_name": "19", \n+      "logic_name": "ensembl_havana_gene", \n+      "object_type": "Gene", \n+      "start": 7112255, \n+      "id": "ENSG00000171105", \n+      "source": "ensembl_havana", \n+      "db_type": "core", \n+      "version": 13, \n+      "biotype": "protein_coding", \n+      "end": 7294034, \n+      "Transcript": [\n+         {\n+            "assembly_name": "GRCh38", \n+            "display_name": "INSR-002", \n+            "Parent": "ENSG00000171105", \n+            "seq_region_name": "19", \n+            "logic_name": "ensembl_havana_transcript", \n+            "object_type": "Transcript", \n+            "start": 7112255, \n+            "id": "ENST00000341500", \n+            "source": "ensembl_havana", \n+            "version": 9, \n+            "Exon": [\n+               {\n+                  "assembly_name": "GRCh38", \n+                  "end": 7293931, \n+                  "start": 7293792, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSE00003071904", \n+                  "seq_region_name": "19", \n+                  "version": 1, \n+                  "species": "homosapiens", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "GRCh38", \n+                  "end": 7267896, \n+                  "start": 7267345, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSE00003664284", \n+                  "seq_region_name": "19", \n+                  "version": 1, \n+                  "species": "homosapiens", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "GRCh38", \n+                  "end": 7184637, \n+                  "start": 7184316, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSE00003682994", \n+                  "seq_region_name": "19", \n+                  "version": 1, \n+                  "species": "homosapiens", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "GRCh38", \n+                  "end": 7174731, \n+                  "start": 7174583, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSE00003659630", \n+                  "seq_region_name": "19", \n+                  "version": 1, \n+                  "species": "homosapiens", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "GRCh38", \n+                  "end": 7172434, \n+                  "start": 7172290, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSE00003580729", \n+                  "seq_region_name": "19", \n+                  "version": 1, \n+                  "species": "homosapiens", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "GRCh38", \n+                  "end": 7170751, \n+                  "start": 7170537, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSE00003536394", \n+                  "seq_region_name": "19", \n+                  "version": 1, \n+                  "species": "homosapiens", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "GRCh38", \n+                  "end": 7168094, \n+                  "start": 7167968, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSE00003613738", \n+                  "seq_region_name": "19", \n+                  "version": 1, \n+                  "speci'..b'                "version": 1, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "CanFam3.1", \n+                  "end": 14518681, \n+                  "start": 14518563, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSCAFE00000177706", \n+                  "seq_region_name": "6", \n+                  "version": 1, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "CanFam3.1", \n+                  "end": 14518488, \n+                  "start": 14518302, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSCAFE00000177713", \n+                  "seq_region_name": "6", \n+                  "version": 1, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "CanFam3.1", \n+                  "end": 14518095, \n+                  "start": 14518022, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSCAFE00000177726", \n+                  "seq_region_name": "6", \n+                  "version": 1, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "CanFam3.1", \n+                  "end": 14517147, \n+                  "start": 14517045, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSCAFE00000177737", \n+                  "seq_region_name": "6", \n+                  "version": 1, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "CanFam3.1", \n+                  "end": 14516938, \n+                  "start": 14516840, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSCAFE00000177744", \n+                  "seq_region_name": "6", \n+                  "version": 1, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "CanFam3.1", \n+                  "end": 14516681, \n+                  "start": 14516506, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSCAFE00000177753", \n+                  "seq_region_name": "6", \n+                  "version": 1, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }, \n+               {\n+                  "assembly_name": "CanFam3.1", \n+                  "end": 14516182, \n+                  "start": 14515204, \n+                  "db_type": "core", \n+                  "object_type": "Exon", \n+                  "id": "ENSCAFE00000177757", \n+                  "seq_region_name": "6", \n+                  "version": 2, \n+                  "species": "canisfamiliaris", \n+                  "strand": -1\n+               }\n+            ], \n+            "biotype": "protein_coding", \n+            "species": "canisfamiliaris", \n+            "end": 14529569, \n+            "Translation": {\n+               "end": 14528678, \n+               "Parent": "ENSCAFT00000025950", \n+               "db_type": "core", \n+               "object_type": "Translation", \n+               "id": "ENSCAFP00000024092", \n+               "start": 14515481, \n+               "length": 824, \n+               "species": "canisfamiliaris"\n+            }, \n+            "is_canonical": "1", \n+            "db_type": "core", \n+            "strand": -1\n+         }\n+      ], \n+      "species": "canisfamiliaris", \n+      "strand": -1\n+   }\n+}\n'
b
diff -r 267a94f068d7 -r 58c9294400ed test-data/gene_family.gafa.sqlite
b
Binary file test-data/gene_family.gafa.sqlite has changed
b
diff -r 267a94f068d7 -r 58c9294400ed test-data/gene_feature.json
--- a/test-data/gene_feature.json Mon Feb 20 12:57:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,1 +0,0 @@\n-{"ENSLAFG00000015027":{"source":"ensembl","object_type":"Gene","logic_name":"ensembl","version":4,"species":"loxodonta_africana","description":"monoamine oxidase B [Source:HGNC Symbol;Acc:HGNC:6834]","display_name":"MAOB","assembly_name":"loxAfr3","biotype":"protein_coding","end":8461554,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFG00000015027","Transcript":[{"source":"ensembl","object_type":"Transcript","logic_name":"ensembl","Exon":[{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8283461,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000459909","start":8283416},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8338115,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173531","start":8338021},{"object_type":"Exon","version":2,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8341774,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173534","start":8341637},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8408659,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173536","start":8408555},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8409483,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173539","start":8409392},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8416102,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173541","start":8415961},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8419821,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000434658","start":8419672},{"object_type":"Exon","version":2,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8425193,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173545","start":8425034},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8432657,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173546","start":8432561},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8433736,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173551","start":8433683},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8454283,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000173554","start":8454226},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8456058,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000397917","start":8455961},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8459456,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000418648","start":8459345},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8460355,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000457038","start":8460293},{"object_type":"Exon","version":1,"species":"loxodonta_africana","assembly_name":"loxAfr3","end":8461545,"seq_region_name":"scaffold_56","db_type":"core","strand":1,"id":"ENSLAFE00000421609","start":8461405}],"Parent":"ENSLAFG00000015027","seq_region_name":"scaffold_56","db_type":"core","is_canonical":"1","strand":1,"id":"ENSLAFT00000015029","version":4,"species":"loxodonta_africana","assembly_name":"loxAfr3","display_name":"MAOB-201","end":8461545,"biotype":"protein_coding","Translation":{"object_type":"Translation","species":"loxodonta_africana","Parent":"ENSLAFT00000015029","end":8461545,"leng'..b'IE00000146839","start":8848740},{"object_type":"Exon","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","end":8847608,"seq_region_name":"JH224647.1","db_type":"core","strand":-1,"id":"ENSPSIE00000147034","start":8847512},{"object_type":"Exon","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","end":8845684,"seq_region_name":"JH224647.1","db_type":"core","strand":-1,"id":"ENSPSIE00000147293","start":8845631},{"object_type":"Exon","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","end":8844627,"seq_region_name":"JH224647.1","db_type":"core","strand":-1,"id":"ENSPSIE00000147543","start":8844570},{"object_type":"Exon","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","end":8844130,"seq_region_name":"JH224647.1","db_type":"core","strand":-1,"id":"ENSPSIE00000147753","start":8844033},{"object_type":"Exon","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","end":8843148,"seq_region_name":"JH224647.1","db_type":"core","strand":-1,"id":"ENSPSIE00000147969","start":8843037},{"object_type":"Exon","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","end":8838545,"seq_region_name":"JH224647.1","db_type":"core","strand":-1,"id":"ENSPSIE00000148136","start":8838483},{"object_type":"Exon","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","end":8837055,"seq_region_name":"JH224647.1","db_type":"core","strand":-1,"id":"ENSPSIE00000148509","start":8835560}],"Parent":"ENSPSIG00000015202","seq_region_name":"JH224647.1","db_type":"core","is_canonical":"1","strand":-1,"id":"ENSPSIT00000017454","version":1,"species":"pelodiscus_sinensis","assembly_name":"PelSin_1.0","display_name":"MAOA-202","end":8874615,"biotype":"protein_coding","Translation":{"object_type":"Translation","species":"pelodiscus_sinensis","Parent":"ENSPSIT00000017454","end":8874615,"length":530,"db_type":"core","id":"ENSPSIP00000017375","start":8836900},"start":8835560}],"start":8832411},"ENSOGAG00000025343":{"source":"ensembl","object_type":"Gene","logic_name":"ensembl","version":1,"species":"otolemur_garnettii","description":"Uncharacterized protein  [Source:UniProtKB/TrEMBL;Acc:H0XT62]","assembly_name":"OtoGar3","biotype":"protein_coding","end":35300936,"seq_region_name":"GL873521.1","db_type":"core","strand":-1,"id":"ENSOGAG00000025343","Transcript":[{"source":"ensembl","object_type":"Transcript","logic_name":"ensembl","Exon":[{"object_type":"Exon","version":1,"species":"otolemur_garnettii","assembly_name":"OtoGar3","end":35300936,"seq_region_name":"GL873521.1","db_type":"core","strand":-1,"id":"ENSOGAE00000326371","start":35300907},{"object_type":"Exon","version":1,"species":"otolemur_garnettii","assembly_name":"OtoGar3","end":35300894,"seq_region_name":"GL873521.1","db_type":"core","strand":-1,"id":"ENSOGAE00000235273","start":35300691},{"object_type":"Exon","version":1,"species":"otolemur_garnettii","assembly_name":"OtoGar3","end":35300688,"seq_region_name":"GL873521.1","db_type":"core","strand":-1,"id":"ENSOGAE00000251114","start":35300617},{"object_type":"Exon","version":1,"species":"otolemur_garnettii","assembly_name":"OtoGar3","end":35300614,"seq_region_name":"GL873521.1","db_type":"core","strand":-1,"id":"ENSOGAE00000316960","start":35300339},{"object_type":"Exon","version":1,"species":"otolemur_garnettii","assembly_name":"OtoGar3","end":35300290,"seq_region_name":"GL873521.1","db_type":"core","strand":-1,"id":"ENSOGAE00000327248","start":35300045}],"Parent":"ENSOGAG00000025343","seq_region_name":"GL873521.1","db_type":"core","is_canonical":"1","strand":-1,"id":"ENSOGAT00000031973","version":1,"species":"otolemur_garnettii","assembly_name":"OtoGar3","end":35300936,"biotype":"protein_coding","Translation":{"object_type":"Translation","species":"otolemur_garnettii","Parent":"ENSOGAT00000031973","end":35300936,"length":275,"db_type":"core","id":"ENSOGAP00000019304","start":35300045},"start":35300045}],"start":35300045}}\n'
b
diff -r 267a94f068d7 -r 58c9294400ed test-data/species.nhx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/species.nhx Fri May 12 11:50:14 2017 -0400
b
@@ -0,0 +1,1 @@
+(((pantroglodytes*,homosapiens*)prim,(rattusnorvegicus*,musmusculus*)rod)euarc,(canisfamiliaris*,susscrofa*)laur)mamm;
b
diff -r 267a94f068d7 -r 58c9294400ed test-data/species_tree.nhx
--- a/test-data/species_tree.nhx Mon Feb 20 12:57:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,1 +0,0 @@
-(((((((((((((((((homosapiens*,gorillagorilla*,pantroglodytes*)207598,pongoabelii*)9604,nomascusleucogenys*)314295,(chlorocebussabaeus*,macacamulatta*,papioanubis*)9528)9526,callithrixjacchus*)314293,tarsiussyrichta*)376913,(microcebusmurinus*,otolemurgarnettii*)376911)9443,((oryctolaguscuniculus*,ochotonaprinceps*)9975,(((rattusnorvegicus*,musmusculus*)39107,dipodomysordii*,ictidomystridecemlineatus*)33553,caviaporcellus*)9989)314147,tupaiabelangeri*)314146,((myotislucifugus*,pteropusvampyrus*)9397,((ovisaries*,bostaurus*)9895,vicugnapacos*,susscrofa*,tursiopstruncatus*)91561,((ailuropodamelanoleuca*,canisfamiliaris*,mustelaputoriusfuro*)379584,feliscatus*)33554,(erinaceuseuropaeus*,sorexaraneus*)9362,equuscaballus*)314145)1437010,(dasypusnovemcinctus*,choloepushoffmanni*)9348,(echinopstelfairi*,loxodontaafricana*,procaviacapensis*)311790)9347,(macropuseugenii*,sarcophilusharrisii*,monodelphisdomestica*)9263)32525,ornithorhynchusanatinus*)40674,((pelodiscussinensis*,(((meleagrisgallopavo*,gallusgallus*)9005,anasplatyrhynchos*)1549675,(ficedulaalbicollis*,taeniopygiaguttata*)9126)8825)1329799,anoliscarolinensis*)32561)32524,xenopustropicalis*)32523,latimeriachalumnae*)8287,(((daniorerio*,astyanaxmexicanus*)186626,((((tetraodonnigroviridis*,takifugurubripes*)31031,gasterosteusaculeatus*)1489922,(((poeciliaformosa*,xiphophorusmaculatus*)586240,oryziaslatipes*)1489913,oreochromisniloticus*)1489908)1489872,gadusmorhua*)123368)186625,lepisosteusoculatus*)41665)117571,petromyzonmarinus*)root;