diff --git a/src/components/pages/ClinHome.vue b/src/components/pages/ClinHome.vue
index 88d6ef3..38b6452 100644
--- a/src/components/pages/ClinHome.vue
+++ b/src/components/pages/ClinHome.vue
@@ -140,6 +140,7 @@ $horizontal-dashboard-height: 140px
:cohortModel="cohortModel"
:launchedFromMosaic="launchedFromMosaic"
@custom-model-info="customModelInfo"
+ @setPhenotypeText="setPhenotypeText($event)"
@setGeneSet="setGeneSet($event)"
@set-ped-data="setPedData($event)"
@set-custom-case-summary="setCustomCaseSummary($event)"
@@ -633,12 +634,13 @@ export default {
cohortModel: null,
customData: false,
customGeneSet: [],
+ customPhenotypeText: "",
bedFileUrl: '',
variantsAnalyzedCounted: 0,
customSavedAnalysis: false,
passcode: '',
showPassCode: false,
- buildName: 'GRCh37',
+ buildName: 'GRCh38',
knownGenesData: null,
byPassedGenes: [],
byPassedGenesDialog: false,
@@ -835,7 +837,7 @@ export default {
self.globalApp.initServices();
self.genomeBuildHelper = new GenomeBuildHelper(self.globalApp);
- return self.genomeBuildHelper.promiseInit({DEFAULT_BUILD: 'GRCh37'})
+ return self.genomeBuildHelper.promiseInit({DEFAULT_BUILD: 'GRCh38'})
})
.then(function() {
if (self.paramBuild && self.paramBuild.length > 0) {
@@ -843,8 +845,8 @@ export default {
self.setBuildName(self.paramBuild);
} else {
// TODO - genome build is required
- self.genomeBuildHelper.setCurrentBuild("GRCh37");
- self.setBuildName("GRCh37");
+ self.genomeBuildHelper.setCurrentBuild("GRCh38");
+ self.setBuildName("GRCh38");
}
let glyph = new Glyph();
@@ -961,8 +963,8 @@ export default {
getDemoVcf: function() {
return {
- 'exome': "https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome.vcf.gz",
- 'genome': "https://s3.amazonaws.com/iobio/gene/wgs_platinum/platinum-trio.vcf.gz"
+ 'exome': "https://iobio.s3.amazonaws.com/samples/vcf/2021_platinum/2021_platinum_exomes_GRCh38.vcf.gz",
+ 'genome': "https://iobio.s3.amazonaws.com/samples/vcf/2021_platinum/2021_platinum_genomes_GRCh38.vcf.gz"
}
},
@@ -970,15 +972,15 @@ export default {
return {
'exome': {
- 'proband': 'https://s3.amazonaws.com/iobio/samples/bam/NA12878.exome.bam',
- 'mother': 'https://s3.amazonaws.com/iobio/samples/bam/NA12892.exome.bam',
- 'father': 'https://s3.amazonaws.com/iobio/samples/bam/NA12891.exome.bam',
- 'sibling': 'https://s3.amazonaws.com/iobio/samples/bam/NA12877.exome.bam'
+ 'proband': 'https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12878.cram',
+ 'mother': 'https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12892.cram',
+ 'father': 'https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12891.cram',
+ 'sibling': 'https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12877.cram'
},
'genome': {
- 'proband': 'https://s3.amazonaws.com/iobio/gene/wgs_platinum/NA12878.bam',
- 'mother': 'https://s3.amazonaws.com/iobio/gene/wgs_platinum/NA12892.bam',
- 'father': 'https://s3.amazonaws.com/iobio/gene/wgs_platinum/NA12891.bam'
+ 'proband': 'https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_genomes/NA12878.cram',
+ 'mother': 'https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_genomes/NA12892.cram',
+ 'father': 'https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_genomes/NA12891.cram'
}
}
@@ -1017,7 +1019,7 @@ export default {
else if(self.customData){
self.$ga.event('launch_type', 'Standalone', 'Custom data');
self.analysis = analysisData;
- self.analysis.payload.demoTextNote = ""
+ self.analysis.payload.demoTextNote = self.customPhenotypeText
self.idAnalysis = self.analysis.id;
if(!self.importedCustomVariants){
self.analysis.payload.variants = [];
@@ -2540,6 +2542,9 @@ export default {
this.customGeneSet = geneSet;
this.setCustomGeneSet(this.customGeneSet);
},
+ setPhenotypeText(phenotypeText){
+ this.customPhenotypeText = phenotypeText;
+ },
setPedData(pedigree){
this.rawPedigree = pedigree;
},
diff --git a/src/components/pages/LandingPage.vue b/src/components/pages/LandingPage.vue
index 5ea148a..030646c 100644
--- a/src/components/pages/LandingPage.vue
+++ b/src/components/pages/LandingPage.vue
@@ -42,7 +42,7 @@
clin.iobio makes it easy to review sequencing and case metrics, generate a prioritized list of genes associated with the disease/phenotype, review candidate variants, and generate a report of your findings
-
+
explore
Run with demo data
@@ -860,6 +860,21 @@ export default {
this.$ga.event('data_type', 'Custom Data', 'Files');
this.getStarted();
},
+ onLoadDemoDataFromConfig: function() {
+ let self = this;
+ this.promiseFetchDemoInputConfig()
+ .then(function() {
+ self.geneSet = ['PRX', 'LMNA', 'SCN8A', 'DLL4', 'ABCA3', 'MROH8', 'DVL3', 'NOTCH4']
+ self.$emit('setGeneSet', self.geneSet)
+ self.$emit("setPhenotypeText", "Charcot-Marie-Tooth disease; demyelination; Dejerine sottas disease possibly; sensory neuropathy; hammertoes; difficulty walking")
+ self.$ga.event('data_type', 'Custom Data', 'Config File');
+ self.getStarted();
+
+ })
+ .catch(function() {
+ alert("Unable to load demo data")
+ })
+ },
onLoadInputConfig: function(){
this.importConfigurationDialog = false;
if(this.genes.length && this.autocompleteGenesConfigFlag===false){
@@ -962,9 +977,6 @@ export default {
this.analysisInProgress = true;
this.setAnalysisInProgressStatus(this.analysisInProgress);
bus.$emit("initialize-clin");
- if(e === 'demo'){
- this.$ga.event('data_type', 'Demo Data', 'Demo dataset');
- }
},
updateCarousel(payload) {
var currentSlide;
@@ -1061,8 +1073,38 @@ export default {
}
return bool;
+ },
+ promiseFetchDemoInputConfig() {
+ let self = this;
+ return new Promise(function(resolve, reject) {
+ let url = "https://iobio.s3.amazonaws.com/clin.iobio/example_file_config_GRCh37.csv"
+ fetch(url)
+ .then(res => {
+ if(!res.ok){
+ console.log("Unable to fetch demo config data file " + url);
+ reject()
+ }
+ else {
+ return res.text();
+ }
+ })
+ .then(data => {
+ console.log(data)
+ self.dataInputConfig = data
+ self.parseInputConfig(data)
+ self.validateSavedConfig = true
+ resolve()
+ })
+ .catch(error => {
+ console.log(error)
+ reject()
+ })
+
+ })
+
},
onInputConfig(ev) {
+ let self = this;
var reader = new FileReader();
if(this.dataInputConfig){
this.validationErrors = [];
@@ -1070,72 +1112,75 @@ export default {
reader.readAsText(this.dataInputConfig);
reader.onload = () => {
let data = reader.result.trim();
- if(this.validateHeadersOfConfigFile(data)){
- let newLine = data.split('\n');
- let headers = newLine.splice(0,4)
- let pedData = [];
- let modelInfoData = [];
- let bedFileUrl = 'https://raw.githubusercontent.com/chmille4/bam.iobio.io/vue/client/data/20130108.exome.targets.bed';
- let buildName = 'GRCh37';
- this.caseTitle = headers[0].split('E:')[1].trim();
- this.caseDescription = headers[1].split('N:')[1].trim();
- let bedFile = headers[2].split('L:')[1].trim().split(",")[0];
- if(bedFile !== ''){
- bedFileUrl = bedFile;
- }
-
- let build = headers[3].split('D:')[1].trim();
- if(build !== ''){
- buildName = build;
- }
-
- let sexMap = {
- "1": "male",
- "2": "female",
- "other": "unknown"
- }
- let statusMap = {
- "0": false,
- "1": false,
- "2": true,
- "-9": false
- }
+ self.parseInputConfig(data)
+ }
+ }
+ },
+ parseInputConfig(data) {
+ if(this.validateHeadersOfConfigFile(data)){
+ let newLine = data.split('\n');
+ let headers = newLine.splice(0,4)
+ let pedData = [];
+ let modelInfoData = [];
+ let bedFileUrl = 'https://iobio.s3.amazonaws.com/clin.iobio/20130108.exome.targets.grch38.bed';
+ let buildName = 'GRCh38';
+ this.caseTitle = headers[0].split('E:')[1].trim();
+ this.caseDescription = headers[1].split('N:')[1].trim();
+ let bedFile = headers[2].split('L:')[1].trim().split(",")[0];
+ if(bedFile !== ''){
+ bedFileUrl = bedFile;
+ }
+
+ let build = headers[3].split('D:')[1].trim();
+ if(build !== ''){
+ buildName = build;
+ }
+
+ let sexMap = {
+ "1": "male",
+ "2": "female",
+ "other": "unknown"
+ }
+ let statusMap = {
+ "0": false,
+ "1": false,
+ "2": true,
+ "-9": false
+ }
+
+ if(this.validateInputConfig(data)){
+ for (var i = 0; i < newLine.length; i++) {
+ var pedLines = newLine[i].split(/\s+|\,/g).slice(0,6);
+ pedData.push(pedLines.join(' '));
- if(this.validateInputConfig(data)){
- for (var i = 0; i < newLine.length; i++) {
- var pedLines = newLine[i].split(/\s+|\,/g).slice(0,6);
- pedData.push(pedLines.join(' '));
-
- var modelInfoLines = newLine[i].split(/\s+|\,/g).slice();
- if(i!==0){
- modelInfoLines[4] = sexMap[modelInfoLines[4]];
- modelInfoLines[5] = statusMap[modelInfoLines[5]];
- }
- modelInfoData.push(modelInfoLines);
- }
- modelInfoData.shift();
- let pedFile = pedData.join('\n');
-
- this.formatCustomModelInfo(modelInfoData);
- this.$emit("setBedFileUrl", bedFileUrl);
- this.$emit("set-ped-data", pedFile);
- this.$emit('setBuildForCustomData', buildName);
- this.$emit("set-custom-case-summary", {
- name: this.caseTitle,
- description: this.caseDescription
- })
- }
- else {
- this.validationErrors.push("Headers do not match with the specified file format. Please check the configuration file and try again.")
- this.dataInputConfig = null;
+ var modelInfoLines = newLine[i].split(/\s+|\,/g).slice();
+ if(i!==0){
+ modelInfoLines[4] = sexMap[modelInfoLines[4]];
+ modelInfoLines[5] = statusMap[modelInfoLines[5]];
}
+ modelInfoData.push(modelInfoLines);
}
- else{
- this.validationErrors.push("Headers do not match with the specified file format. Please check the configuration file and try again.")
- this.dataInputConfig = null;
- }
+ modelInfoData.shift();
+ let pedFile = pedData.join('\n');
+
+ this.formatCustomModelInfo(modelInfoData);
+ this.$emit("setBedFileUrl", bedFileUrl);
+ this.$emit("set-ped-data", pedFile);
+ this.$emit('setBuildForCustomData', buildName);
+ this.$emit("set-custom-case-summary", {
+ name: this.caseTitle,
+ description: this.caseDescription
+ })
+ }
+ else {
+ this.validationErrors.push("Headers do not match with the specified file format. Please check the configuration file and try again.")
+ this.dataInputConfig = null;
}
}
+ else{
+ this.validationErrors.push("Headers do not match with the specified file format. Please check the configuration file and try again.")
+ this.dataInputConfig = null;
+ }
},
formatCustomModelInfo(modelInfoData){
var modelInfo = [];
diff --git a/src/components/viz/ReviewCase.vue b/src/components/viz/ReviewCase.vue
index 5b06533..7c84f74 100644
--- a/src/components/viz/ReviewCase.vue
+++ b/src/components/viz/ReviewCase.vue
@@ -631,7 +631,6 @@ export default {
}
}
else{
- this.overridePropsWithDemoData();
this.buildPage();
}
@@ -1114,16 +1113,6 @@ export default {
this.coverageHistosData = this.coverageHistos;
},
- overridePropsWithDemoData(){
- this.pedigreeData ={"0":{"id":3261,"metrics":{"second_mates":"16534422","test2_77850c8c":"15","proper_pairs":"99.1149","failed_qc":"0","strand_bias":"1.00551","ts_tv_ratio":"2.05896","variant_count":"88110","pedigree":"Pedigree","var_other_count":"4124","duplicate_rate":"0.00348412","affected_status":"Unaffected","file_location":"s3","both_mates_mapped":"32943377","var_snp_count":"77618","singletons":"55024","var_indel_count":"8672","first_mates":"16503521","total_reads":"33037943","mapped_reads":"32998401","read_coverage_iqr":"15","paired_end_reads":"33037943","median_read_coverage":"51"},"distributions":{"chrom_coverage":"null","mut_spec":{"A":[0,12636,4063,1854],"G":[13569,0,3808,2863],"C":[2901,3961,0,13330],"T":[1833,4091,12709,0]},"af_hist":{"usingLogScaleAF":false,"afHistBins":{"6":17695,"8":206,"12":9919,"16":203,"18":10661,"25":11775,"31":8610,"33":156,"37":7772,"41":104,"43":6914}},"coverage_hist":{"quartiles":[59,51,44],"whiskers":[74,29]},"length_hist":{"quartiles":[101,101,101],"whiskers":[101,101]},"frag_hist":{"quartiles":[363,319,277],"whiskers":[449,191]},"mapq_hist":{"quartiles":[60,60,60],"whiskers":[60,60]},"coverage_hist_no_outliers":{"29":0.004871,"30":0.005242,"31":0.005779,"32":0.006489,"33":0.007382,"34":0.008438,"35":0.009793,"36":0.011365,"37":0.013201,"38":0.015237,"39":0.017403,"40":0.019552,"41":0.021913,"42":0.024191,"43":0.026483,"44":0.028585,"45":0.030652,"46":0.032406,"47":0.033824,"48":0.035041,"49":0.035973,"50":0.036446,"51":0.036685,"52":0.036585,"53":0.036086,"54":0.035348,"55":0.034207,"56":0.032812,"57":0.031296,"58":0.029653,"59":0.027818,"60":0.02603,"61":0.02397,"62":0.02191,"63":0.019862,"64":0.017845,"65":0.016009,"66":0.014165,"67":0.012458,"68":0.010852,"69":0.009428,"70":0.008084,"71":0.006864,"72":0.00579,"73":0.004839,"74":0.003993}},"uid":"0ced8131-34f","name":"NA12877.exome","description":null,"ancestry":{"background":604,"data":[-0.1026610208789221,-1.4242045534784185,"EUR"]},"created_at":"2019-07-18T15:12:05.413Z","updated_at":"2019-07-18T15:12:05.413Z","kindred_id":50,"sample_id":3261,"paternal_id":3263,"maternal_id":3264,"sex":1,"affection_status":1,"client_name":"11002","pedigree":{"kindred_id":"b537452d-9852-4605-8fd5-c90635d2824c","sample_id":3261,"paternal_id":3263,"maternal_id":3264,"sex":1,"affection_status":1},"vcf_sample_name":"NA12877","files":{"bam":"https://s3.amazonaws.com/iobio/samples/bam/NA12877.exome.bam","tbi":"https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome_NA12877.vcf.gz.tbi","vcf":"https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome_NA12877.vcf.gz","bai":"https://s3.amazonaws.com/iobio/samples/bam/NA12877.exome.bam.bai"}},"1":{"id":3262,"metrics":{"duplicate_rate":"0.00414535","ts_tv_ratio":"2.14514","first_mates":"16282871","total_reads":"32568521","var_indel_count":"8816","var_other_count":"4006","singletons":"87747","file_location":"s3","strand_bias":"1.0064","mapped_reads":"32505279","second_mates":"16285650","pedigree":"Pedigree","median_read_coverage":"50","read_coverage_iqr":"13","variant_count":"86759","failed_qc":"0","proper_pairs":"98.8382","var_snp_count":"76210","paired_end_reads":"32568521","both_mates_mapped":"32417532","affected_status":"Affected"},"distributions":{"chrom_coverage":"null","mut_spec":{"A":[0,12505,3647,1839],"G":[13474,0,3814,2815],"C":[2882,3847,0,13423],"T":[1858,3529,12577,0]},"af_hist":{"usingLogScaleAF":false,"afHistBins":{"6":2095,"8":124,"12":16045,"16":165,"18":13794,"25":14207,"31":10273,"33":177,"37":8805,"41":93,"43":6914}},"coverage_hist":{"quartiles":[57,50,44],"whiskers":[70,31]},"length_hist":{"quartiles":[101,101,101],"whiskers":[101,101]},"frag_hist":{"quartiles":[366,321,277],"whiskers":[455,188]},"mapq_hist":{"quartiles":[60,60,60],"whiskers":[60,60]},"coverage_hist_no_outliers":{"31":0.004288,"32":0.005304,"33":0.00659,"34":0.008097,"35":0.009874,"36":0.01195,"37":0.014323,"38":0.01694,"39":0.019677,"40":0.022559,"41":0.025512,"42":0.028514,"43":0.031331,"44":0.034076,"45":0.036573,"46":0.038604,"47":0.040373,"48":0.04158,"49":0.042213,"50":0.042424,"51":0.042139,"52":0.041356,"53":0.040086,"54":0.038539,"55":0.036649,"56":0.03441,"57":0.032007,"58":0.029539,"59":0.026872,"60":0.024301,"61":0.021637,"62":0.019012,"63":0.01666,"64":0.014452,"65":0.012375,"66":0.01055,"67":0.008907,"68":0.007446,"69":0.006186,"70":0.005052}},"uid":"72de2cd5-97f","name":"NA12878.exome","description":null,"ancestry":{"background":604,"data":[-0.31801863225785604,-1.4812542726924995,"EUR"]},"created_at":"2019-07-18T15:12:05.413Z","updated_at":"2019-07-18T15:12:05.413Z","kindred_id":50,"sample_id":3262,"paternal_id":3263,"maternal_id":3264,"sex":2,"affection_status":2,"client_name":"11002","pedigree":{"kindred_id":"b537452d-9852-4605-8fd5-c90635d2824c","sample_id":3262,"paternal_id":3263,"maternal_id":3264,"sex":2,"affection_status":2},"vcf_sample_name":"NA12878","files":{"bam":"https://s3.amazonaws.com/iobio/samples/bam/NA12878.exome.bam","bai":"https://s3.amazonaws.com/iobio/samples/bam/NA12878.exome.ba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-
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- },
-
sortData(){
diff --git a/src/data/example_file_config_GRCh37.csv b/src/data/example_file_config_GRCh37.csv
new file mode 100644
index 0000000..9ce092a
--- /dev/null
+++ b/src/data/example_file_config_GRCh37.csv
@@ -0,0 +1,9 @@
+#PROJECT_NAME: Demo project
+#PROJECT_DESCRIPTION: Exome sequencing project for four samples.
+#BED_URL: https://iobio.s3.amazonaws.com/clin.iobio/20130108.exome.targets.bed
+#BUILD: GRCh37
+ID,SAMPLE_ID,PATERNAL_ID,MATERNAL_ID,SEX,AFFECTED_STATUS,RELATION,VCF_URL,TBI_URL,BAM_URL,BAI_URL
+1,NA12878,NA12891,NA12892,1,2,proband,https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome.vcf.gz,,https://s3.amazonaws.com/iobio/samples/bam/NA12878.exome.bam,
+1,NA12877,NA12891,NA12892,2,1,sibling,https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome.vcf.gz,,https://s3.amazonaws.com/iobio/samples/bam/NA12877.exome.bam,
+1,NA12891,0,0,1,1,father,https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome.vcf.gz,,https://s3.amazonaws.com/iobio/samples/bam/NA12892.exome.bam,
+1,NA12892,0,0,2,1,mother,https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome.vcf.gz,,https://s3.amazonaws.com/iobio/samples/bam/NA12891.exome.bam,
\ No newline at end of file
diff --git a/src/data/example_file_config_GRCh38.csv b/src/data/example_file_config_GRCh38.csv
index 9deff09..118daf5 100644
--- a/src/data/example_file_config_GRCh38.csv
+++ b/src/data/example_file_config_GRCh38.csv
@@ -1,5 +1,5 @@
-#PROJECT_NAME: demo project GRCh38
-#PROJECT_DESCRIPTION: Exome sequencing project for three samples.
+#PROJECT_NAME: Example project
+#PROJECT_DESCRIPTION: Exome sequencing project for four samples.
#BED_URL: https://iobio.s3.amazonaws.com/clin.iobio/20130108.exome.targets.grch38.bed
#BUILD: GRCh38
ID,SAMPLE_ID,PATERNAL_ID,MATERNAL_ID,SEX,AFFECTED_STATUS,RELATION,VCF_URL,TBI_URL,BAM_URL,BAI_URL