Bug fixes, including typos in standard data file and corrupted/trunca…

…ted reference genome. Adding additional radar plot to report showing bias based on relative abundance.
Zymo-Research · Jan 17, 2020 · db9ef98 · db9ef98
1 parent 94ede02
commit db9ef98
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Showing 5 changed files with 822,883 additions and 9 deletions.
diff --git a/analyzeStandardReads.py b/analyzeStandardReads.py
@@ -197,14 +197,33 @@ def saveResult(result:miqScoreNGSReadCountPublic.MiqScoreData):
     return outputFilePath
 
 
+def generateReportReplacementTable(sampleMiq, goodExampleMiq, badExampleMiq, readFatePrintNames:dict=None):
+    readFateTable = miqScoreShotgunPublicSupport.reporting.generateReadFateChartBody(miqScoreShotgunPublicSupport.reporting.generateAbsoluteReadFateCounts(sampleMiq), readFatePrintNames)
+    replacementTable = {"SAMPLENAME": sampleMiq.sampleID,
+                        "MIQSCORE": str(round(sampleMiq.miqScore)),
+                        "READFATETABLE": readFateTable,
+                        "READFATECHART": sampleMiq.plots["readFates"],
+                        "COMPOSITIONBARPLOT": sampleMiq.plots["compositionPlot"],
+                        "GOODRADARPLOTLYSIS": goodExampleMiq.plots["radarPlots"]["Lysis Difficulty"],
+                        "SAMPLERADARPLOTLYSIS": sampleMiq.plots["radarPlots"]["Lysis Difficulty"],
+                        "BADRADARPLOTLYSIS": badExampleMiq.plots["radarPlots"]["Lysis Difficulty"],
+                        "GOODRADARPLOTABUNDANCE": goodExampleMiq.plots["radarPlots"]["Abundance"],
+                        "SAMPLERADARPLOTABUNDANCE": sampleMiq.plots["radarPlots"]["Abundance"],
+                        "BADRADARPLOTABUNDANCE": badExampleMiq.plots["radarPlots"]["Abundance"],
+                        "GOODRADARPLOTGC": goodExampleMiq.plots["radarPlots"]["GC Content"],
+                        "SAMPLERADARPLOTGC": sampleMiq.plots["radarPlots"]["GC Content"],
+                        "BADRADARPLOTGC": badExampleMiq.plots["radarPlots"]["GC Content"]}
+    return replacementTable
+
+
 def generateReport(result:miqScoreNGSReadCountPublic.MiqScoreData):
     referenceData = miqScoreNGSReadCountPublic.referenceHandler.StandardReference(parameters.referenceDataFile.value)
     templateFilePath = os.path.join(os.path.split(os.path.abspath(__file__))[0], "reference", "shotgunReportTemplate.html")
     templateFile = open(templateFilePath, 'r')
     template = templateFile.read()
     templateFile.close()
     goodMiq, badMiq = miqScoreNGSReadCountPublic.loadExampleData(parameters.goodMiqExample.value, parameters.badMiqExample.value, referenceData, "Genomic")
-    replacementTable = miqScoreShotgunPublicSupport.reporting.generateReplacementTable(result, goodMiq, badMiq, readFatePrintNames=readFatePrintNames)
+    replacementTable = generateReportReplacementTable(result, goodMiq, badMiq, readFatePrintNames=readFatePrintNames)
     report = miqScoreNGSReadCountPublic.reportGeneration.generateReport(template, replacementTable)
     reportFilePath = os.path.join(parameters.outputFolder.value, "%s.html" % parameters.sampleName.value)
     print("Output report to %s" % reportFilePath)
@@ -230,7 +249,7 @@ def generateReport(result:miqScoreNGSReadCountPublic.MiqScoreData):
     logger.debug("Starting analysis")
     bamFilePath = os.path.join(parameters.outputFolder.value, "%s.bam" %parameters.sampleName.value)
     if applicationMode == "PE":
-        miqScoreShotgunPublicSupport.alignmentAnalysis.bwaHandler.bwaAlignPE(parameters.forwardReads.value, parameters.reverseReads.value, parameters.workingFolder.value, bamFilePath, parameters.referenceGenome.value)
+        #miqScoreShotgunPublicSupport.alignmentAnalysis.bwaHandler.bwaAlignPE(parameters.forwardReads.value, parameters.reverseReads.value, parameters.workingFolder.value, bamFilePath, parameters.referenceGenome.value) #TODO Return this line to functionality if disabled
         readTable = miqScoreShotgunPublicSupport.alignmentAnalysis.alignmentAnalysisPE.bamFileProcessor(bamFilePath)
     elif applicationMode == "SE":
         miqScoreShotgunPublicSupport.alignmentAnalysis.bwaHandler.bwaAlignSE(parameters.reads.value, parameters.workingFolder.value, bamFilePath, parameters.referenceGenome.value)

diff --git a/defaults/environment.py b/defaults/environment.py
@@ -12,7 +12,7 @@
 reverseReads = os.path.join(sequenceFolder, "standard_submitted_R2.fastq")
 referenceFolder = os.path.join(os.path.split(__main__.__file__)[0], "reference")
 referenceGenome = os.path.join(referenceFolder, "zrGutStandard.fasta")
-#referenceGenome = "/opt/miqScoreShotgun/reference/zrGutStandard.fa" #for external debugging
+#referenceGenome = "/opt/miqScoreShotgun/reference/zrGutStandard.fasta" #for external debugging
 referenceDataFile = os.path.join(referenceFolder, "zrGutStandard.json")
 goodMiqExample = os.path.join(referenceFolder, "goodMiq.json")
 badMiqExample = os.path.join(referenceFolder, "badMiq.json")

diff --git a/reference/shotgunReportTemplate.html b/reference/shotgunReportTemplate.html
@@ -22,6 +22,8 @@ <h3><strong>MIQ (Measurement Integrity Quotient Score)</strong></h3>
 <h3><strong>Bias Detection (Radar) Plots</strong></h3>
 <table border="0" style="border-collapse: collapse; width: 100%; margin-left: auto; margin-right: auto;">
 <tbody>
+
+
 <tr>
 <td style="width: 33.3333%;">
 <p><img src="data:image/png;base64,%%GOODRADARPLOTLYSIS%%" alt="Good Example Radar Plot" width="395" height="296" caption="false" style="display: block; margin-left: auto; margin-right: auto;" /></p>
@@ -38,6 +40,20 @@ <h3><strong>Bias Detection (Radar) Plots</strong></h3>
 </tr>
 <tr>
 <td style="width: 33.3333%;">
+<p><img src="data:image/png;base64,%%GOODRADARPLOTABUNDANCE%%" alt="Good Example Radar Plot" width="395" height="296" caption="false" style="display: block; margin-left: auto; margin-right: auto;" /></p>
+<p style="text-align: center;">Good (Example)</p>
+</td>
+<td style="width: 33.3333%; text-align: center;">
+<p><img src="data:image/png;base64,%%SAMPLERADARPLOTABUNDANCE%%" alt="Your Sample" width="395" height="296" caption="false" /></p>
+<p><strong>%%SAMPLENAME%%</strong></p>
+</td>
+<td style="width: 33.3333%; text-align: center;">
+<p><img src="data:image/png;base64,%%BADRADARPLOTABUNDANCE%%" alt="Bad Example Radar Plot" width="395" height="296" caption="false" /></p>
+<p>Biased (Example)</p>
+</td>
+</tr>
+<tr>
+<td style="width: 33.3333%;">
 <p><img src="data:image/png;base64,%%GOODRADARPLOTGC%%" alt="Good Example Radar Plot" width="395" height="296" caption="false" style="display: block; margin-left: auto; margin-right: auto;" /></p>
 <p style="text-align: center;">Good (Example)</p>
 </td>