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Show top100 features for metaT #295

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merged 1 commit into from
Sep 4, 2024
Merged

Show top100 features for metaT #295

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2 changes: 1 addition & 1 deletion webapp/client/src/pipelines/MetaT/Workflow/Results/Metatranscriptome.js
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ function Metatranscriptome(props) {
<Annotation title={'Annotation Result'} result={props.result['annotation-stats']} userType={props.type} allExpand={props.allExpand} allClosed={props.allClosed} />
}
{props.result['readMapping-features'] &&
<ReadMapping title={'Read Mapping Result'} project={props.project} tooLarge={props.result['readMapping-features-too-large']} features={props.result['readMapping-features']} userType={props.type} allExpand={props.allExpand} allClosed={props.allClosed} />
<ReadMapping title={'Read Mapping Result'} project={props.project} tooLarge={props.result['readMapping-features-too-large']} features={props.result['readMapping-features']} topFeatures={props.result['readMapping-top_features']} userType={props.type} allExpand={props.allExpand} allClosed={props.allClosed} />
}
</>
);
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4 changes: 4 additions & 0 deletions webapp/client/src/pipelines/MetaT/Workflow/Results/ReadMapping.js
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,10 @@ function ReadMapping(props) {
<br></br>
<a href={url + props.features} target="_blank" rel="noreferrer" >[ Export the result as TSV ]</a>
<br></br><br></br>
Top 100 features
<br></br>
<FeaturesTable data={props.topFeatures} />
<br></br>
</>
: <>
<FeaturesTable data={props.features} />
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51 changes: 19 additions & 32 deletions webapp/server/util/workflow.js
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Original file line number Diff line number Diff line change
Expand Up @@ -189,26 +189,18 @@ const generateWorkflowResult = function (proj) {
} else if (workflowConf.workflow.name === 'Metatranscriptome') {
const dirs = fs.readdirSync(outdir);
dirs.forEach(function (dir) {
if (dir === 'qa') {
const files = fs.readdirSync(outdir + "/qa");
if (dir === 'qa' || dir === 'readsQC') {
const files = fs.readdirSync(outdir + "/" + dir);
files.forEach(function (file) {
if (file.endsWith("_stats.json")) {
result['readsQC-stats'] = JSON.parse(fs.readFileSync(outdir + "/qa/" + file));
}
});
}
if (dir === 'readsQC') {
const files = fs.readdirSync(outdir + "/readsQC");
files.forEach(function (file) {
if (file.endsWith("_stats.json")) {
result['readsQC-stats'] = JSON.parse(fs.readFileSync(outdir + "/readsQC/" + file));
result['readsQC-stats'] = JSON.parse(fs.readFileSync(outdir + "/" + dir + "/" + file));
}
});
}
else if (dir === 'assembly') {
const files = fs.readdirSync(outdir + "/assembly");
files.forEach(function (file) {
if (file.endsWith("_stats.json")) {
if (file.endsWith("stats.json")) {
result['assembly-stats'] = JSON.parse(fs.readFileSync(outdir + "/assembly/" + file));
}
});
Expand All @@ -221,32 +213,27 @@ const generateWorkflowResult = function (proj) {
}
});
}
else if (dir === 'metat_output') {
const files = fs.readdirSync(outdir + "/metat_output");
else if (dir === 'metat_output' || dir === 'readMapping') {
const files = fs.readdirSync(outdir + "/" + dir);
files.forEach(function (file) {
if (file.endsWith("_sorted_features.tsv")) {
var rows = parseInt(execSync("wc -l < " + outdir + "/metat_output/" + file).toString().trim());
if (rows > config.IO.MAX_DATATABLE_ROWS) {
result['readMapping-features-too-large'] = true;
result['readMapping-features'] = "output/Metatranscriptomics/metat_output/" + file;
} else {
result['readMapping-features-too-large'] = false;
result['readMapping-features'] = Papa.parse(fs.readFileSync(outdir + "/metat_output/" + file).toString(), { delimiter: '\t', header: true, skipEmptyLines: true }).data;
if (file.endsWith("sorted_features.tsv")) {
const jsonFile = file.replace('.tsv', '.json');
let topFeatures = "top100_features.json";
if (!fs.existsSync(outdir + "/" + dir + "/" + topFeatures)) {
topFeatures = file.replace('_sorted_features.tsv', '_top100_features.json');
}
}
});
}
else if (dir === 'readMapping') {
const files = fs.readdirSync(outdir + "/readMapping");
files.forEach(function (file) {
if (file.endsWith("_sorted_features.tsv")) {
var rows = parseInt(execSync("wc -l < " + outdir + "/readMapping/" + file).toString().trim());
var rows = parseInt(execSync("wc -l < " + outdir + "/" + dir + "/" + file).toString().trim());
if (rows > config.IO.MAX_DATATABLE_ROWS) {
result['readMapping-features-too-large'] = true;
result['readMapping-features'] = "output/Metatranscriptomics/readMapping/" + file;
result['readMapping-features'] = "output/Metatranscriptomics/" + dir + "/" + file;
result['readMapping-top_features'] = JSON.parse(fs.readFileSync(outdir + "/" + dir + "/" + topFeatures));
} else {
result['readMapping-features-too-large'] = false;
result['readMapping-features'] = Papa.parse(fs.readFileSync(outdir + "/readMapping/" + file).toString(), { delimiter: '\t', header: true, skipEmptyLines: true }).data;
if (fs.existsSync(outdir + "/" + dir + "/" + jsonFile)) {
result['readMapping-features'] = JSON.parse(fs.readFileSync(outdir + "/" + dir + "/" + jsonFile));
} else {
result['readMapping-features'] = Papa.parse(fs.readFileSync(outdir + "/" + dir + "/" + file).toString(), { delimiter: '\t', header: true, skipEmptyLines: true }).data;
}
}
}
});
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