diff test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json @ 0:be6cec883b02 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gff3_to_json commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty
author earlhaminst
date Wed, 21 Dec 2016 10:02:59 -0500
parents
children befe6021e476
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json	Wed Dec 21 10:02:59 2016 -0500
@@ -0,0 +1,343 @@
+{
+   "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
+   }
+}