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Merge pull request #640 from TheJacksonLaboratory/update-output-formats
Enhance output formats
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -11,8 +11,6 @@ | |
| import org.monarchinitiative.phenol.ontology.data.MinimalOntology; | ||
| import org.monarchinitiative.phenol.ontology.data.Term; | ||
| import org.monarchinitiative.phenol.ontology.data.TermId; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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||
| import java.io.IOException; | ||
| import java.nio.file.Files; | ||
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@@ -27,7 +25,6 @@ | |
| * @author <a href="mailto:[email protected]">Peter Robinson</a> | ||
| */ | ||
| public abstract class LiricalTemplate { | ||
| private static final Logger logger = LoggerFactory.getLogger(LiricalTemplate.class); | ||
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| private final AnalysisData analysisData; | ||
| /** Map of data that will be used for the FreeMark template. */ | ||
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@@ -75,7 +72,7 @@ private void initTemplateData(AnalysisData analysisData, | |
| String tstr = String.format("%s <a href=\"https://hpo.jax.org/app/browse/term/%s\">%s</a>",termName,id.getValue(),id.getValue()); | ||
| observedHPOs.add(tstr); | ||
| } | ||
| this.templateData.put("observedHPOs",observedHPOs); | ||
| templateData.put("observedHPOs",observedHPOs); | ||
| List<String> excludedHpos = new ArrayList<>(); | ||
| for (TermId id:analysisData.negatedPhenotypeTerms()) { | ||
| String termName = ontology.termForTermId(id) | ||
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@@ -84,12 +81,10 @@ private void initTemplateData(AnalysisData analysisData, | |
| String tstr = String.format("%s <a href=\"https://hpo.jax.org/app/browse/term/%s\">%s</a>",termName,id.getValue(),id.getValue()); | ||
| excludedHpos.add(tstr); | ||
| } | ||
| this.templateData.put("excludedHPOs",excludedHpos); | ||
| // This is a flag for the output to only show the list if there are some phenotypes that were excluded in the | ||
| // proband. | ||
| if (!excludedHpos.isEmpty()) { | ||
| this.templateData.put("hasExcludedHPOs","true"); | ||
| } | ||
| templateData.put("excludedHPOs",excludedHpos); | ||
| // Indicates that LIRICAL was run without a VCF file. | ||
| templateData.put("phenotypeOnly", analysisData.genes().size() == 0); | ||
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|
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| } | ||
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| /** Some of our name strings contain multiple synonyms. This function removes all but the first.*/ | ||
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@@ -101,8 +96,6 @@ protected String shortName(String name) { | |
| return name; | ||
| } | ||
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| public Path getOutPath() { return outputPath;} | ||
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| protected static Path createOutputFile(Path outdir, String prefix, String format) { | ||
| if (!Files.isDirectory(outdir)) | ||
| mkdirIfNotExist(outdir); | ||
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||
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25 changes: 20 additions & 5 deletions
25
lirical-io/src/main/resources/org/monarchinitiative/lirical/io/output/liricalTSV.ftl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,26 @@ | ||
| ! LIRICAL TSV Output (${resultsMeta.liricalVersion}) | ||
| ! Sample: ${resultsMeta.sampleName!"n/a"} | ||
| ! Observed HPO terms | ||
| <#if observedHPOs?has_content> | ||
| ! Observed HPO terms: | ||
| <#list observedHPOs as obs_hpo> | ||
| ! ${obs_hpo} | ||
| </#list> | ||
| </#if> | ||
| <#if excludedHPOs?has_content> | ||
| ! Excluded HPO terms: | ||
| <#list excludedHPOs as ex_hpo> | ||
| ! ${ex_hpo} | ||
| </#list> | ||
| </#if> | ||
| <#assign tab="\t"> | ||
| <#list observedHPOs as hpo> | ||
| ! ${hpo} | ||
| <#if phenotypeOnly> | ||
| rank${tab}diseaseName${tab}diseaseCurie${tab}pretestprob${tab}posttestprob${tab}compositeLR | ||
| <#list diff as dd> | ||
| ${dd.rank}${tab}${dd.diseaseName}${tab}${dd.diseaseCurie}${tab}${dd.pretestprob}${tab}${dd.posttestprob}${tab}${dd.compositeLR} | ||
| </#list> | ||
| ${header} | ||
| <#else> | ||
| rank${tab}diseaseName${tab}diseaseCurie${tab}pretestprob${tab}posttestprob${tab}compositeLR${tab}${tab}entrezGeneId${tab}variants | ||
| <#list diff as dd> | ||
| ${dd.rank}${tab}${dd.diseaseName}${tab}${dd.diseaseCurie}${tab}${dd.pretestprob}${tab}${dd.posttestprob}${tab}${dd.compositeLR}${tab}${dd.entrezGeneId}${tab}${dd.varString} | ||
| </#list> | ||
| </#list> | ||
| </#if> |