diff test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json @ 1:befe6021e476 draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gff3_to_json commit 5e5fbe362ed5a4714debda0f2c0834cbbfd34147
author earlhaminst
date Tue, 28 Feb 2017 12:06:04 -0500
parents be6cec883b02
children
line wrap: on
line diff
--- a/test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json	Wed Dec 21 10:02:59 2016 -0500
+++ b/test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json	Tue Feb 28 12:06:04 2017 -0500
@@ -1,343 +1,1 @@
-{
-   "gene:WBGene00022276": {
-      "Name": "nlp-40", 
-      "Transcript": [
-         {
-            "Exon": [
-               {
-                  "Name": "Y74C9A.2a.2.e1", 
-                  "Parent": "transcript:Y74C9A.2a.2", 
-                  "constitutive": "0", 
-                  "end": 10585, 
-                  "ensembl_end_phase": "-1", 
-                  "ensembl_phase": "-1", 
-                  "exon_id": "Y74C9A.2a.2.e1", 
-                  "id": "Y74C9A.2a.2.e1", 
-                  "length": 173, 
-                  "object_type": "Exon", 
-                  "rank": "1", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 10413, 
-                  "strand": 1
-               }, 
-               {
-                  "Name": "Y74C9A.2a.1.e1", 
-                  "Parent": "transcript:Y74C9A.2a.2", 
-                  "constitutive": "0", 
-                  "end": 11689, 
-                  "ensembl_end_phase": "1", 
-                  "ensembl_phase": "-1", 
-                  "exon_id": "Y74C9A.2a.1.e1", 
-                  "id": "Y74C9A.2a.1.e1", 
-                  "length": 72, 
-                  "object_type": "Exon", 
-                  "rank": "2", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 11618, 
-                  "strand": 1
-               }, 
-               {
-                  "Name": "Y74C9A.2a.1.e2", 
-                  "Parent": "transcript:Y74C9A.2a.2", 
-                  "constitutive": "0", 
-                  "end": 15160, 
-                  "ensembl_end_phase": "1", 
-                  "ensembl_phase": "1", 
-                  "exon_id": "Y74C9A.2a.1.e2", 
-                  "id": "Y74C9A.2a.1.e2", 
-                  "length": 210, 
-                  "object_type": "Exon", 
-                  "rank": "3", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 14951, 
-                  "strand": 1
-               }, 
-               {
-                  "Name": "Y74C9A.2a.1.e3", 
-                  "Parent": "transcript:Y74C9A.2a.2", 
-                  "constitutive": "0", 
-                  "end": 16842, 
-                  "ensembl_end_phase": "-1", 
-                  "ensembl_phase": "1", 
-                  "exon_id": "Y74C9A.2a.1.e3", 
-                  "id": "Y74C9A.2a.1.e3", 
-                  "length": 370, 
-                  "object_type": "Exon", 
-                  "rank": "4", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 16473, 
-                  "strand": 1
-               }
-            ], 
-            "Name": "Y74C9A.2a.2", 
-            "Parent": "gene:WBGene00022276", 
-            "Translation": {
-               "CDS": [
-                  {
-                     "Parent": "transcript:Y74C9A.2a.2", 
-                     "end": 11689, 
-                     "id": "CDS:Y74C9A.2a.2", 
-                     "protein_id": "Y74C9A.2a.2", 
-                     "start": 11641, 
-                     "strand": 1
-                  }, 
-                  {
-                     "Parent": "transcript:Y74C9A.2a.2", 
-                     "end": 15160, 
-                     "id": "CDS:Y74C9A.2a.2", 
-                     "protein_id": "Y74C9A.2a.2", 
-                     "start": 14951, 
-                     "strand": 1
-                  }, 
-                  {
-                     "Parent": "transcript:Y74C9A.2a.2", 
-                     "end": 16585, 
-                     "id": "CDS:Y74C9A.2a.2", 
-                     "protein_id": "Y74C9A.2a.2", 
-                     "start": 16473, 
-                     "strand": 1
-                  }
-               ], 
-               "end": 16585, 
-               "id": "CDS:Y74C9A.2a.2", 
-               "object_type": "Translation", 
-               "species": "caenorhabditiselegans", 
-               "start": 11641
-            }, 
-            "biotype": "protein_coding", 
-            "end": 16842, 
-            "id": "transcript:Y74C9A.2a.2", 
-            "object_type": "Transcript", 
-            "seq_region_name": "I", 
-            "species": "caenorhabditiselegans", 
-            "start": 10413, 
-            "strand": 1, 
-            "transcript_id": "Y74C9A.2a.2"
-         }
-      ], 
-      "biotype": "protein_coding", 
-      "description": "Neuropeptide-Like Protein  [Source:RefSeq peptide%3BAcc:NP_001293206]", 
-      "end": 16842, 
-      "gene_id": "WBGene00022276", 
-      "id": "gene:WBGene00022276", 
-      "logic_name": "wormbase", 
-      "member_id": 0, 
-      "object_type": "Gene", 
-      "seq_region_name": "I", 
-      "species": "caenorhabditiselegans", 
-      "start": 10413, 
-      "strand": 1
-   }, 
-   "gene:WBGene00022278": {
-      "Name": "rcor-1", 
-      "Transcript": [
-         {
-            "Exon": [
-               {
-                  "Name": "Y74C9A.4a.e12", 
-                  "Parent": "transcript:Y74C9A.4d", 
-                  "constitutive": "1", 
-                  "end": 17958, 
-                  "ensembl_end_phase": "-1", 
-                  "ensembl_phase": "0", 
-                  "exon_id": "Y74C9A.4a.e12", 
-                  "id": "Y74C9A.4a.e12", 
-                  "length": 476, 
-                  "object_type": "Exon", 
-                  "rank": "7", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 17483, 
-                  "strand": -1
-               }, 
-               {
-                  "Name": "Y74C9A.4a.e11", 
-                  "Parent": "transcript:Y74C9A.4d", 
-                  "constitutive": "1", 
-                  "end": 18115, 
-                  "ensembl_end_phase": "0", 
-                  "ensembl_phase": "1", 
-                  "exon_id": "Y74C9A.4a.e11", 
-                  "id": "Y74C9A.4a.e11", 
-                  "length": 110, 
-                  "object_type": "Exon", 
-                  "rank": "6", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 18006, 
-                  "strand": -1
-               }, 
-               {
-                  "Name": "Y74C9A.4a.e10", 
-                  "Parent": "transcript:Y74C9A.4d", 
-                  "constitutive": "1", 
-                  "end": 19241, 
-                  "ensembl_end_phase": "1", 
-                  "ensembl_phase": "2", 
-                  "exon_id": "Y74C9A.4a.e10", 
-                  "id": "Y74C9A.4a.e10", 
-                  "length": 227, 
-                  "object_type": "Exon", 
-                  "rank": "5", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 19015, 
-                  "strand": -1
-               }, 
-               {
-                  "Name": "Y74C9A.4a.e9", 
-                  "Parent": "transcript:Y74C9A.4d", 
-                  "constitutive": "1", 
-                  "end": 20478, 
-                  "ensembl_end_phase": "2", 
-                  "ensembl_phase": "1", 
-                  "exon_id": "Y74C9A.4a.e9", 
-                  "id": "Y74C9A.4a.e9", 
-                  "length": 208, 
-                  "object_type": "Exon", 
-                  "rank": "4", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 20271, 
-                  "strand": -1
-               }, 
-               {
-                  "Name": "Y74C9A.4a.e8", 
-                  "Parent": "transcript:Y74C9A.4d", 
-                  "constitutive": "1", 
-                  "end": 20964, 
-                  "ensembl_end_phase": "1", 
-                  "ensembl_phase": "1", 
-                  "exon_id": "Y74C9A.4a.e8", 
-                  "id": "Y74C9A.4a.e8", 
-                  "length": 117, 
-                  "object_type": "Exon", 
-                  "rank": "3", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 20848, 
-                  "strand": -1
-               }, 
-               {
-                  "Name": "Y74C9A.4d.e2", 
-                  "Parent": "transcript:Y74C9A.4d", 
-                  "constitutive": "0", 
-                  "end": 21136, 
-                  "ensembl_end_phase": "1", 
-                  "ensembl_phase": "-1", 
-                  "exon_id": "Y74C9A.4d.e2", 
-                  "id": "Y74C9A.4d.e2", 
-                  "length": 124, 
-                  "object_type": "Exon", 
-                  "rank": "2", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 21013, 
-                  "strand": -1
-               }, 
-               {
-                  "Name": "Y74C9A.4d.e1", 
-                  "Parent": "transcript:Y74C9A.4d", 
-                  "constitutive": "0", 
-                  "end": 24796, 
-                  "ensembl_end_phase": "-1", 
-                  "ensembl_phase": "-1", 
-                  "exon_id": "Y74C9A.4d.e1", 
-                  "id": "Y74C9A.4d.e1", 
-                  "length": 146, 
-                  "object_type": "Exon", 
-                  "rank": "1", 
-                  "seq_region_name": "I", 
-                  "species": "caenorhabditiselegans", 
-                  "start": 24651, 
-                  "strand": -1
-               }
-            ], 
-            "Name": "Y74C9A.4d", 
-            "Parent": "gene:WBGene00022278", 
-            "Translation": {
-               "CDS": [
-                  {
-                     "Parent": "transcript:Y74C9A.4d", 
-                     "end": 17958, 
-                     "id": "CDS:Y74C9A.4d", 
-                     "protein_id": "Y74C9A.4d", 
-                     "start": 17911, 
-                     "strand": -1
-                  }, 
-                  {
-                     "Parent": "transcript:Y74C9A.4d", 
-                     "end": 18115, 
-                     "id": "CDS:Y74C9A.4d", 
-                     "protein_id": "Y74C9A.4d", 
-                     "start": 18006, 
-                     "strand": -1
-                  }, 
-                  {
-                     "Parent": "transcript:Y74C9A.4d", 
-                     "end": 19241, 
-                     "id": "CDS:Y74C9A.4d", 
-                     "protein_id": "Y74C9A.4d", 
-                     "start": 19015, 
-                     "strand": -1
-                  }, 
-                  {
-                     "Parent": "transcript:Y74C9A.4d", 
-                     "end": 20478, 
-                     "id": "CDS:Y74C9A.4d", 
-                     "protein_id": "Y74C9A.4d", 
-                     "start": 20271, 
-                     "strand": -1
-                  }, 
-                  {
-                     "Parent": "transcript:Y74C9A.4d", 
-                     "end": 20964, 
-                     "id": "CDS:Y74C9A.4d", 
-                     "protein_id": "Y74C9A.4d", 
-                     "start": 20848, 
-                     "strand": -1
-                  }, 
-                  {
-                     "Parent": "transcript:Y74C9A.4d", 
-                     "end": 21127, 
-                     "id": "CDS:Y74C9A.4d", 
-                     "protein_id": "Y74C9A.4d", 
-                     "start": 21013, 
-                     "strand": -1
-                  }
-               ], 
-               "end": 21127, 
-               "id": "CDS:Y74C9A.4d", 
-               "object_type": "Translation", 
-               "species": "caenorhabditiselegans", 
-               "start": 17911
-            }, 
-            "biotype": "protein_coding", 
-            "end": 24796, 
-            "id": "transcript:Y74C9A.4d", 
-            "object_type": "Transcript", 
-            "seq_region_name": "I", 
-            "species": "caenorhabditiselegans", 
-            "start": 17483, 
-            "strand": -1, 
-            "transcript_id": "Y74C9A.4d"
-         }
-      ], 
-      "biotype": "protein_coding", 
-      "description": "RCOR (REST CO-Repressor) homolog  [Source:RefSeq peptide%3BAcc:NP_001293207]", 
-      "end": 26781, 
-      "gene_id": "WBGene00022278", 
-      "id": "gene:WBGene00022278", 
-      "logic_name": "wormbase", 
-      "member_id": 1, 
-      "object_type": "Gene", 
-      "seq_region_name": "I", 
-      "species": "caenorhabditiselegans", 
-      "start": 17483, 
-      "strand": -1
-   }
-}
+{"WBGene00022276": {"Name": "nlp-40", "Transcript": [{"Exon": [{"Name": "Y74C9A.2a.2.e1", "Parent": "Y74C9A.2a.2", "constitutive": "0", "end": 10585, "ensembl_end_phase": "-1", "ensembl_phase": "-1", "exon_id": "Y74C9A.2a.2.e1", "id": "Y74C9A.2a.2.e1", "length": 173, "object_type": "Exon", "rank": "1", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 10413, "strand": 1}, {"Name": "Y74C9A.2a.1.e1", "Parent": "Y74C9A.2a.2", "constitutive": "0", "end": 11689, "ensembl_end_phase": "1", "ensembl_phase": "-1", "exon_id": "Y74C9A.2a.1.e1", "id": "Y74C9A.2a.1.e1", "length": 72, "object_type": "Exon", "rank": "2", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 11618, "strand": 1}, {"Name": "Y74C9A.2a.1.e2", "Parent": "Y74C9A.2a.2", "constitutive": "0", "end": 15160, "ensembl_end_phase": "1", "ensembl_phase": "1", "exon_id": "Y74C9A.2a.1.e2", "id": "Y74C9A.2a.1.e2", "length": 210, "object_type": "Exon", "rank": "3", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 14951, "strand": 1}, {"Name": "Y74C9A.2a.1.e3", "Parent": "Y74C9A.2a.2", "constitutive": "0", "end": 16842, "ensembl_end_phase": "-1", "ensembl_phase": "1", "exon_id": "Y74C9A.2a.1.e3", "id": "Y74C9A.2a.1.e3", "length": 370, "object_type": "Exon", "rank": "4", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 16473, "strand": 1}], "Name": "Y74C9A.2a.2", "Parent": "WBGene00022276", "Translation": {"CDS": [{"Parent": "Y74C9A.2a.2", "end": 11689, "id": "Y74C9A.2a.2", "protein_id": "Y74C9A.2a.2", "start": 11641, "strand": 1}, {"Parent": "Y74C9A.2a.2", "end": 15160, "id": "Y74C9A.2a.2", "protein_id": "Y74C9A.2a.2", "start": 14951, "strand": 1}, {"Parent": "Y74C9A.2a.2", "end": 16585, "id": "Y74C9A.2a.2", "protein_id": "Y74C9A.2a.2", "start": 16473, "strand": 1}], "end": 16585, "id": "Y74C9A.2a.2", "object_type": "Translation", "species": "caenorhabditiselegans", "start": 11641}, "biotype": "protein_coding", "end": 16842, "id": "Y74C9A.2a.2", "object_type": "Transcript", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 10413, "strand": 1, "transcript_id": "Y74C9A.2a.2"}], "biotype": "protein_coding", "description": "Neuropeptide-Like Protein  [Source:RefSeq peptide%3BAcc:NP_001293206]", "end": 16842, "gene_id": "WBGene00022276", "id": "WBGene00022276", "logic_name": "wormbase", "member_id": 0, "object_type": "Gene", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 10413, "strand": 1}, "WBGene00022278": {"Name": "rcor-1", "Transcript": [{"Exon": [{"Name": "Y74C9A.4a.e12", "Parent": "Y74C9A.4d", "constitutive": "1", "end": 17958, "ensembl_end_phase": "-1", "ensembl_phase": "0", "exon_id": "Y74C9A.4a.e12", "id": "Y74C9A.4a.e12", "length": 476, "object_type": "Exon", "rank": "7", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 17483, "strand": -1}, {"Name": "Y74C9A.4a.e11", "Parent": "Y74C9A.4d", "constitutive": "1", "end": 18115, "ensembl_end_phase": "0", "ensembl_phase": "1", "exon_id": "Y74C9A.4a.e11", "id": "Y74C9A.4a.e11", "length": 110, "object_type": "Exon", "rank": "6", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 18006, "strand": -1}, {"Name": "Y74C9A.4a.e10", "Parent": "Y74C9A.4d", "constitutive": "1", "end": 19241, "ensembl_end_phase": "1", "ensembl_phase": "2", "exon_id": "Y74C9A.4a.e10", "id": "Y74C9A.4a.e10", "length": 227, "object_type": "Exon", "rank": "5", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 19015, "strand": -1}, {"Name": "Y74C9A.4a.e9", "Parent": "Y74C9A.4d", "constitutive": "1", "end": 20478, "ensembl_end_phase": "2", "ensembl_phase": "1", "exon_id": "Y74C9A.4a.e9", "id": "Y74C9A.4a.e9", "length": 208, "object_type": "Exon", "rank": "4", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 20271, "strand": -1}, {"Name": "Y74C9A.4a.e8", "Parent": "Y74C9A.4d", "constitutive": "1", "end": 20964, "ensembl_end_phase": "1", "ensembl_phase": "1", "exon_id": "Y74C9A.4a.e8", "id": "Y74C9A.4a.e8", "length": 117, "object_type": "Exon", "rank": "3", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 20848, "strand": -1}, {"Name": "Y74C9A.4d.e2", "Parent": "Y74C9A.4d", "constitutive": "0", "end": 21136, "ensembl_end_phase": "1", "ensembl_phase": "-1", "exon_id": "Y74C9A.4d.e2", "id": "Y74C9A.4d.e2", "length": 124, "object_type": "Exon", "rank": "2", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 21013, "strand": -1}, {"Name": "Y74C9A.4d.e1", "Parent": "Y74C9A.4d", "constitutive": "0", "end": 24796, "ensembl_end_phase": "-1", "ensembl_phase": "-1", "exon_id": "Y74C9A.4d.e1", "id": "Y74C9A.4d.e1", "length": 146, "object_type": "Exon", "rank": "1", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 24651, "strand": -1}], "Name": "Y74C9A.4d", "Parent": "WBGene00022278", "Translation": {"CDS": [{"Parent": "Y74C9A.4d", "end": 17958, "id": "Y74C9A.4d", "protein_id": "Y74C9A.4d", "start": 17911, "strand": -1}, {"Parent": "Y74C9A.4d", "end": 18115, "id": "Y74C9A.4d", "protein_id": "Y74C9A.4d", "start": 18006, "strand": -1}, {"Parent": "Y74C9A.4d", "end": 19241, "id": "Y74C9A.4d", "protein_id": "Y74C9A.4d", "start": 19015, "strand": -1}, {"Parent": "Y74C9A.4d", "end": 20478, "id": "Y74C9A.4d", "protein_id": "Y74C9A.4d", "start": 20271, "strand": -1}, {"Parent": "Y74C9A.4d", "end": 20964, "id": "Y74C9A.4d", "protein_id": "Y74C9A.4d", "start": 20848, "strand": -1}, {"Parent": "Y74C9A.4d", "end": 21127, "id": "Y74C9A.4d", "protein_id": "Y74C9A.4d", "start": 21013, "strand": -1}], "end": 21127, "id": "Y74C9A.4d", "object_type": "Translation", "species": "caenorhabditiselegans", "start": 17911}, "biotype": "protein_coding", "end": 24796, "id": "Y74C9A.4d", "object_type": "Transcript", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 17483, "strand": -1, "transcript_id": "Y74C9A.4d"}], "biotype": "protein_coding", "description": "RCOR (REST CO-Repressor) homolog  [Source:RefSeq peptide%3BAcc:NP_001293207]", "end": 26781, "gene_id": "WBGene00022278", "id": "WBGene00022278", "logic_name": "wormbase", "member_id": 1, "object_type": "Gene", "seq_region_name": "I", "species": "caenorhabditiselegans", "start": 17483, "strand": -1}}
\ No newline at end of file