@sjcrh/proteinpaint-server 2.44.0 → 2.46.1

package/genome/hg19.js

@@ -1,206 +1,301 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = {
-    species: 'human',
-    genomefile: 'genomes/hg19.gz',
-    genedb: {
-        dbfile: 'anno/genes.hg19.db'
+var hg19_default = {
+  species: "human",
+  genomefile: "genomes/hg19.gz",
+  genedb: {
+    dbfile: "anno/genes.hg19.db"
+  },
+  proteindomain: {
+    dbfile: "anno/db/proteindomain.db",
+    statement: "select data from domain where isoform=? collate nocase"
+  },
+  repeatmasker: {
+    dbfile: "anno/rmsk.hg19.gz",
+    statement: "RepeatMasker database"
+  },
+  snp: {
+    bigbedfile: "anno/dbsnp.hg19.bb"
+  },
+  fimo_motif: {
+    db: "utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme",
+    annotationfile: "utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_annotation_HUMAN_mono.tsv"
+  },
+  tracks: [
+    {
+      __isgene: true,
+      // only for initialization
+      translatecoding: true,
+      // instructs to translate coding:[]
+      file: "anno/refGene.hg19.gz",
+      type: "bedj",
+      name: "RefGene",
+      stackheight: 16,
+      stackspace: 1,
+      vpad: 4,
+      color: "#1D591D"
     },
-    proteindomain: {
-        dbfile: 'anno/db/proteindomain.db',
-        statement: 'select data from domain where isoform=? collate nocase'
+    {
+      __isgene: true,
+      translatecoding: true,
+      file: "anno/gencode.v40.hg19.gz",
+      type: "bedj",
+      name: "GENCODE v40",
+      stackheight: 16,
+      stackspace: 1,
+      vpad: 4,
+      categories: {
+        coding: { color: "#004D99", label: "Coding gene" },
+        nonCoding: { color: "#008833", label: "Noncoding gene" },
+        problem: { color: "#CC3300", label: "Problem" },
+        pseudo: { color: "#CC00CC", label: "Pseudogene" }
+      }
     },
-    repeatmasker: {
-        dbfile: 'anno/rmsk.hg19.gz',
-        statement: 'RepeatMasker database'
+    {
+      type: "bedj",
+      name: "RepeatMasker",
+      stackheight: 14,
+      file: "anno/rmsk.hg19.gz",
+      onerow: true,
+      categories: {
+        SINE: { color: "#ED8C8E", label: "SINE" },
+        LINE: { color: "#EDCB8C", label: "LINE" },
+        LTR: { color: "#E38CED", label: "LTR" },
+        DNA: { color: "#8C8EED", label: "DNA transposon" },
+        simple: { color: "#8EB88C", label: "Simple repeats" },
+        low_complexity: { color: "#ACEBA9", label: "Low complexity" },
+        satellite: { color: "#B59A84", label: "Satellite" },
+        RNA: { color: "#9DE0E0", label: "RNA repeat" },
+        other: { color: "#9BADC2", label: "Other" },
+        unknown: { color: "#858585", label: "Unknown" }
+      }
+    }
+  ],
+  /*
+  geneset: [
+  	{
+  		name: 'Signaling',
+  		lst: [
+  			{ name: 'NRAS' },
+  			{ name: 'FLT3' },
+  			{ name: 'KRAS' },
+  			{ name: 'JAK3' },
+  			{ name: 'BRAF' },
+  			{ name: 'NF1' },
+  			{ name: 'MAPK1' }
+  		]
+  	},
+  	{ name: 'Cell cycle', lst: [{ name: 'TP53' }, { name: 'RB1' }, { name: 'CDKN2A' }, { name: 'CDKN2B' }] },
+  	{
+  		name: 'Epigenetics',
+  		lst: [
+  			{ name: 'ATRX' },
+  			{ name: 'BCOR' },
+  			{ name: 'MYC' },
+  			{ name: 'MYCN' },
+  			{ name: 'WHSC1' },
+  			{ name: 'SUZ12' },
+  			{ name: 'EED' },
+  			{ name: 'EZH2' },
+  			{ name: 'SETD2' },
+  			{ name: 'CREBBP' },
+  			{ name: 'EHMT2' },
+  			{ name: 'PRDM1' },
+  			{ name: 'NSD1' },
+  			{ name: 'KMT2D' },
+  			{ name: 'UBR4' },
+  			{ name: 'ARID1A' },
+  			{ name: 'EP300' }
+  		]
+  	},
+  	{
+  		name: 'Development',
+  		lst: [
+  			{ name: 'RUNX1' },
+  			{ name: 'ETV6' },
+  			{ name: 'GATA3' },
+  			{ name: 'IKZF1' },
+  			{ name: 'EP300' },
+  			{ name: 'IKZF2' },
+  			{ name: 'IKZF3' },
+  			{ name: 'PAX5' },
+  			{ name: 'VPREB1' },
+  			{ name: 'EBF1' }
+  		]
+  	}
+  ],
+  */
+  defaultcoord: {
+    chr: "chr17",
+    start: 7568451,
+    stop: 7591984,
+    gene: "TP53"
+  },
+  hicenzymefragment: [
+    {
+      enzyme: "DpnII",
+      file: "anno/hicFragment/hic.DpnII.hg19.gz"
     },
-    snp: {
-        bigbedfile: 'anno/dbsnp.hg19.bb'
+    {
+      enzyme: "EcoRI",
+      file: "anno/hicFragment/hic.EcoRI.hg19.gz"
     },
-    fimo_motif: {
-        db: 'utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme',
-        annotationfile: 'utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_annotation_HUMAN_mono.tsv'
+    {
+      enzyme: "HindIII",
+      file: "anno/hicFragment/hic.HindIII.hg19.gz"
     },
-    tracks: [
-        {
-            __isgene: true,
-            translatecoding: true,
-            file: 'anno/refGene.hg19.gz',
-            type: 'bedj',
-            name: 'RefGene',
-            stackheight: 16,
-            stackspace: 1,
-            vpad: 4,
-            color: '#1D591D'
-        },
-        {
-            __isgene: true,
-            translatecoding: true,
-            file: 'anno/gencode.v40.hg19.gz',
-            type: 'bedj',
-            name: 'GENCODE v40',
-            stackheight: 16,
-            stackspace: 1,
-            vpad: 4,
-            categories: {
-                coding: { color: '#004D99', label: 'Coding gene' },
-                nonCoding: { color: '#008833', label: 'Noncoding gene' },
-                problem: { color: '#CC3300', label: 'Problem' },
-                pseudo: { color: '#CC00CC', label: 'Pseudogene' }
-            }
-        },
-        {
-            type: 'bedj',
-            name: 'RepeatMasker',
-            stackheight: 14,
-            file: 'anno/rmsk.hg19.gz',
-            onerow: true,
-            categories: {
-                SINE: { color: '#ED8C8E', label: 'SINE' },
-                LINE: { color: '#EDCB8C', label: 'LINE' },
-                LTR: { color: '#E38CED', label: 'LTR' },
-                DNA: { color: '#8C8EED', label: 'DNA transposon' },
-                simple: { color: '#8EB88C', label: 'Simple repeats' },
-                low_complexity: { color: '#ACEBA9', label: 'Low complexity' },
-                satellite: { color: '#B59A84', label: 'Satellite' },
-                RNA: { color: '#9DE0E0', label: 'RNA repeat' },
-                other: { color: '#9BADC2', label: 'Other' },
-                unknown: { color: '#858585', label: 'Unknown' }
-            }
-        }
-    ],
-    /*
-    geneset: [
-        {
-            name: 'Signaling',
-            lst: [
-                { name: 'NRAS' },
-                { name: 'FLT3' },
-                { name: 'KRAS' },
-                { name: 'JAK3' },
-                { name: 'BRAF' },
-                { name: 'NF1' },
-                { name: 'MAPK1' }
-            ]
-        },
-        { name: 'Cell cycle', lst: [{ name: 'TP53' }, { name: 'RB1' }, { name: 'CDKN2A' }, { name: 'CDKN2B' }] },
-        {
-            name: 'Epigenetics',
-            lst: [
-                { name: 'ATRX' },
-                { name: 'BCOR' },
-                { name: 'MYC' },
-                { name: 'MYCN' },
-                { name: 'WHSC1' },
-                { name: 'SUZ12' },
-                { name: 'EED' },
-                { name: 'EZH2' },
-                { name: 'SETD2' },
-                { name: 'CREBBP' },
-                { name: 'EHMT2' },
-                { name: 'PRDM1' },
-                { name: 'NSD1' },
-                { name: 'KMT2D' },
-                { name: 'UBR4' },
-                { name: 'ARID1A' },
-                { name: 'EP300' }
-            ]
-        },
-        {
-            name: 'Development',
-            lst: [
-                { name: 'RUNX1' },
-                { name: 'ETV6' },
-                { name: 'GATA3' },
-                { name: 'IKZF1' },
-                { name: 'EP300' },
-                { name: 'IKZF2' },
-                { name: 'IKZF3' },
-                { name: 'PAX5' },
-                { name: 'VPREB1' },
-                { name: 'EBF1' }
-            ]
-        }
-    ],
-    */
-    defaultcoord: {
-        chr: 'chr17',
-        start: 7568451,
-        stop: 7591984,
-        gene: 'TP53'
+    {
+      enzyme: "MboI",
+      file: "anno/hicFragment/hic.MboI.hg19.gz"
     },
-    hicenzymefragment: [
-        {
-            enzyme: 'DpnII',
-            file: 'anno/hicFragment/hic.DpnII.hg19.gz'
-        },
-        {
-            enzyme: 'EcoRI',
-            file: 'anno/hicFragment/hic.EcoRI.hg19.gz'
-        },
-        {
-            enzyme: 'HindIII',
-            file: 'anno/hicFragment/hic.HindIII.hg19.gz'
-        },
-        {
-            enzyme: 'MboI',
-            file: 'anno/hicFragment/hic.MboI.hg19.gz'
-        },
-        {
-            enzyme: 'NcoI',
-            file: 'anno/hicFragment/hic.NcoI.hg19.gz'
-        }
-    ],
-    hicdomain: {
-        groups: {
-            RaoCell2014: {
-                name: 'Rao SS et al, Cell 2014',
-                reference: '<a href=https://www.ncbi.nlm.nih.gov/pubmed/25497547 target=_blank>A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping</a>',
-                sets: {
-                    GM12878: {
-                        name: 'GM12878',
-                        longname: 'Human B-Lymphoblastoid',
-                        file: 'anno/hicTAD/aiden2014/GM12878.domain.hg19.gz'
-                    },
-                    HMEC: {
-                        name: 'HMEC',
-                        longname: 'Human Mammary Epithelial',
-                        file: 'anno/hicTAD/aiden2014/HMEC.domain.hg19.gz'
-                    },
-                    IMR90: {
-                        name: 'IRM90',
-                        longname: 'Human Lung Fibroblast',
-                        file: 'anno/hicTAD/aiden2014/IMR90.domain.hg19.gz'
-                    },
-                    KBM7: {
-                        name: 'KBM7',
-                        longname: 'Near Haploid Human Myelogenous Leukemia',
-                        file: 'anno/hicTAD/aiden2014/KBM7.domain.hg19.gz'
-                    },
-                    HeLa: {
-                        name: 'HeLa',
-                        longname: 'Human Cervical Carcinoma',
-                        file: 'anno/hicTAD/aiden2014/HeLa.domain.hg19.gz'
-                    },
-                    HUVEC: {
-                        name: 'HUVEC',
-                        longname: 'Human Umbilical Vein Endothelial',
-                        file: 'anno/hicTAD/aiden2014/HUVEC.domain.hg19.gz'
-                    },
-                    K562: {
-                        name: 'K562',
-                        longname: 'Human Erythroleukemia',
-                        file: 'anno/hicTAD/aiden2014/K562.domain.hg19.gz'
-                    },
-                    NHEK: {
-                        name: 'NHEK',
-                        longname: 'Normal Human Epidermal Keratinocytes',
-                        file: 'anno/hicTAD/aiden2014/NHEK.domain.hg19.gz'
-                    }
-                }
-            }
+    {
+      enzyme: "NcoI",
+      file: "anno/hicFragment/hic.NcoI.hg19.gz"
+    }
+  ],
+  hicdomain: {
+    groups: {
+      RaoCell2014: {
+        name: "Rao SS et al, Cell 2014",
+        reference: "<a href=https://www.ncbi.nlm.nih.gov/pubmed/25497547 target=_blank>A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping</a>",
+        sets: {
+          GM12878: {
+            name: "GM12878",
+            longname: "Human B-Lymphoblastoid",
+            file: "anno/hicTAD/aiden2014/GM12878.domain.hg19.gz"
+          },
+          HMEC: {
+            name: "HMEC",
+            longname: "Human Mammary Epithelial",
+            file: "anno/hicTAD/aiden2014/HMEC.domain.hg19.gz"
+          },
+          IMR90: {
+            name: "IRM90",
+            longname: "Human Lung Fibroblast",
+            file: "anno/hicTAD/aiden2014/IMR90.domain.hg19.gz"
+          },
+          KBM7: {
+            name: "KBM7",
+            longname: "Near Haploid Human Myelogenous Leukemia",
+            file: "anno/hicTAD/aiden2014/KBM7.domain.hg19.gz"
+          },
+          HeLa: {
+            name: "HeLa",
+            longname: "Human Cervical Carcinoma",
+            file: "anno/hicTAD/aiden2014/HeLa.domain.hg19.gz"
+          },
+          HUVEC: {
+            name: "HUVEC",
+            longname: "Human Umbilical Vein Endothelial",
+            file: "anno/hicTAD/aiden2014/HUVEC.domain.hg19.gz"
+          },
+          K562: {
+            name: "K562",
+            longname: "Human Erythroleukemia",
+            file: "anno/hicTAD/aiden2014/K562.domain.hg19.gz"
+          },
+          NHEK: {
+            name: "NHEK",
+            longname: "Normal Human Epidermal Keratinocytes",
+            file: "anno/hicTAD/aiden2014/NHEK.domain.hg19.gz"
+          }
         }
-    },
-    majorchr: "chr1\t249250621\nchr2\t243199373\nchr3\t198022430\nchr4\t191154276\nchr5\t180915260\nchr6\t171115067\nchr7\t159138663\nchr8\t146364022\nchr9\t141213431\nchr10\t135534747\nchr11\t135006516\nchr12\t133851895\nchr13\t115169878\nchr14\t107349540\nchr15\t102531392\nchr16\t90354753\nchr17\t81195210\nchr18\t78077248\nchr19\t59128983\nchr20\t63025520\nchr21\t48129895\nchr22\t51304566\nchrX\t155270560\nchrY\t59373566\nchrM\t16571",
-    minorchr: "\nchr6_ssto_hap7\t4928567\nchr6_mcf_hap5\t4833398\nchr6_cox_hap2\t4795371\nchr6_mann_hap4\t4683263\nchr6_apd_hap1\t4622290\nchr6_qbl_hap6\t4611984\nchr6_dbb_hap3\t4610396\nchr17_ctg5_hap1\t1680828\nchr4_ctg9_hap1\t590426\nchr1_gl000192_random\t547496\nchrUn_gl000225\t211173\nchr4_gl000194_random\t191469\nchr4_gl000193_random\t189789\nchr9_gl000200_random\t187035\nchrUn_gl000222\t186861\nchrUn_gl000212\t186858\nchr7_gl000195_random\t182896\nchrUn_gl000223\t180455\nchrUn_gl000224\t179693\nchrUn_gl000219\t179198\nchr17_gl000205_random\t174588\nchrUn_gl000215\t172545\nchrUn_gl000216\t172294\nchrUn_gl000217\t172149\nchr9_gl000199_random\t169874\nchrUn_gl000211\t166566\nchrUn_gl000213\t164239\nchrUn_gl000220\t161802\nchrUn_gl000218\t161147\nchr19_gl000209_random\t159169\nchrUn_gl000221\t155397\nchrUn_gl000214\t137718\nchrUn_gl000228\t129120\nchrUn_gl000227\t128374\nchr1_gl000191_random\t106433\nchr19_gl000208_random\t92689\nchr9_gl000198_random\t90085\nchr17_gl000204_random\t81310\nchrUn_gl000233\t45941\nchrUn_gl000237\t45867\nchrUn_gl000230\t43691\nchrUn_gl000242\t43523\nchrUn_gl000243\t43341\nchrUn_gl000241\t42152\nchrUn_gl000236\t41934\nchrUn_gl000240\t41933\nchr17_gl000206_random\t41001\nchrUn_gl000232\t40652\nchrUn_gl000234\t40531\nchr11_gl000202_random\t40103\nchrUn_gl000238\t39939\nchrUn_gl000244\t39929\nchrUn_gl000248\t39786\nchr8_gl000196_random\t38914\nchrUn_gl000249\t38502\nchrUn_gl000246\t38154\nchr17_gl000203_random\t37498\nchr8_gl000197_random\t37175\nchrUn_gl000245\t36651\nchrUn_gl000247\t36422\nchr9_gl000201_random\t36148\nchrUn_gl000235\t34474\nchrUn_gl000239\t33824\nchr21_gl000210_random\t27682\nchrUn_gl000231\t27386\nchrUn_gl000229\t19913\nchrUn_gl000226\t15008\nchr18_gl000207_random\t4262"
+      }
+    }
+  },
+  majorchr: `chr1	249250621
+chr2	243199373
+chr3	198022430
+chr4	191154276
+chr5	180915260
+chr6	171115067
+chr7	159138663
+chr8	146364022
+chr9	141213431
+chr10	135534747
+chr11	135006516
+chr12	133851895
+chr13	115169878
+chr14	107349540
+chr15	102531392
+chr16	90354753
+chr17	81195210
+chr18	78077248
+chr19	59128983
+chr20	63025520
+chr21	48129895
+chr22	51304566
+chrX	155270560
+chrY	59373566
+chrM	16571`,
+  minorchr: `
+chr6_ssto_hap7	4928567
+chr6_mcf_hap5	4833398
+chr6_cox_hap2	4795371
+chr6_mann_hap4	4683263
+chr6_apd_hap1	4622290
+chr6_qbl_hap6	4611984
+chr6_dbb_hap3	4610396
+chr17_ctg5_hap1	1680828
+chr4_ctg9_hap1	590426
+chr1_gl000192_random	547496
+chrUn_gl000225	211173
+chr4_gl000194_random	191469
+chr4_gl000193_random	189789
+chr9_gl000200_random	187035
+chrUn_gl000222	186861
+chrUn_gl000212	186858
+chr7_gl000195_random	182896
+chrUn_gl000223	180455
+chrUn_gl000224	179693
+chrUn_gl000219	179198
+chr17_gl000205_random	174588
+chrUn_gl000215	172545
+chrUn_gl000216	172294
+chrUn_gl000217	172149
+chr9_gl000199_random	169874
+chrUn_gl000211	166566
+chrUn_gl000213	164239
+chrUn_gl000220	161802
+chrUn_gl000218	161147
+chr19_gl000209_random	159169
+chrUn_gl000221	155397
+chrUn_gl000214	137718
+chrUn_gl000228	129120
+chrUn_gl000227	128374
+chr1_gl000191_random	106433
+chr19_gl000208_random	92689
+chr9_gl000198_random	90085
+chr17_gl000204_random	81310
+chrUn_gl000233	45941
+chrUn_gl000237	45867
+chrUn_gl000230	43691
+chrUn_gl000242	43523
+chrUn_gl000243	43341
+chrUn_gl000241	42152
+chrUn_gl000236	41934
+chrUn_gl000240	41933
+chr17_gl000206_random	41001
+chrUn_gl000232	40652
+chrUn_gl000234	40531
+chr11_gl000202_random	40103
+chrUn_gl000238	39939
+chrUn_gl000244	39929
+chrUn_gl000248	39786
+chr8_gl000196_random	38914
+chrUn_gl000249	38502
+chrUn_gl000246	38154
+chr17_gl000203_random	37498
+chr8_gl000197_random	37175
+chrUn_gl000245	36651
+chrUn_gl000247	36422
+chr9_gl000201_random	36148
+chrUn_gl000235	34474
+chrUn_gl000239	33824
+chr21_gl000210_random	27682
+chrUn_gl000231	27386
+chrUn_gl000229	19913
+chrUn_gl000226	15008
+chr18_gl000207_random	4262`
+};
+export {
+  hg19_default as default
 };