add new KGD plots , remove some no longer needed

AgResearch · Jan 17, 2022 · b5847fb · b5847fb
1 parent 24081f6
commit b5847fb
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/make_clientcohort_pages.py b/make_clientcohort_pages.py
@@ -67,11 +67,10 @@ def generate_run_plot(options):
 
     file_group_iter = (  ("KGD (plots)", "image"), ("KGD (text file links)", "link"), ("Hapmap files", "link" ) )
     file_iters = {
-        "KGD (plots)" : ['AlleleFreq.png', 'CallRate.png', 'Co-call-HWdgm.05.png', 'Co-call-.png', 'finplot.png', 'GcompareHWdgm.05.png', 'Gcompare.png', 'Gdiagdepth.png', 'G-diag.png', 'GHWdgm.05diagdepth.png', 'GHWdgm.05-diag.png', 'Heatmap-G5HWdgm.05.png', 'HWdisMAFsig.png', 'LRT-hist.png', 'LRT-QQ.png', 'MAFHWdgm.05.png', 'MAF.png', 'PC1v2G5HWdgm.05.png', 'SampDepthCR.png', 'SampDepthHist.png', 'SampDepth.png', 'SampDepth-scored.png', 'SNPCallRate.png', 'SNPDepthHist.png', 'SNPDepth.png', 'X2star-QQ.png'],
+        "KGD (plots)" : ['AlleleFreq.png', 'CallRate.png', 'Co-call-HWdgm.05.png', 'Co-call-.png', 'finplot.png', 'GcompareHWdgm.05.png', 'Gcompare.png', 'Gdiagdepth.png', 'GHWdgm.05diagdepth.png', 'InbCompare.png', 'Heatmap-G5HWdgm.05.png', 'HWdisMAFsig.png', 'MAFHWdgm.05.png', 'MAF.png', 'PC1v2G5HWdgm.05.png', 'SampDepthCR.png', 'SampDepthHist.png', 'SampDepth.png', 'SampDepth-scored.png', 'SNPCallRate.png', 'SNPDepthHist.png', 'SNPDepth.png', 'X2star-QQ.png'],
         "KGD (text file links)" : ['GHW05.csv', 'GHW05-Inbreeding.csv', 'GHW05-long.csv', 'GHW05-pca_metadata.tsv', 'GHW05-pca_vectors.tsv', 'GHW05-PC.csv', 'GHW05.RData', 'GHW05.vcf', 'HeatmapOrderHWdgm.05.csv', 'HeatmapOrderHWdgm.05.csv.blinded', 'PCG5HWdgm.05.pdf', 'SampleStats.csv', 'SampleStats.csv.blinded', 'seqID.csv', 'seqID.csv.blinded'],
         "Hapmap files" : ['HapMap.hmc.txt','HapMap.hmp.txt']
     }
-
     file_iters["KGD (plots)"] = [ os.path.join(options["kgd_subfolder_name"], item) for item in file_iters["KGD (plots)"] ]
     file_iters["KGD (text file links)"] = [ os.path.join(options["kgd_subfolder_name"], item) for item in file_iters["KGD (text file links)"] ]
     file_iters["Hapmap files"] = [ os.path.join(options["hapmap_subfolder_name"], item) for item in file_iters["Hapmap files"] ]

diff --git a/make_cohort_pages.py b/make_cohort_pages.py
@@ -173,11 +173,11 @@ def generate_run_plot(options):
         #        'KGD/Co-call-.png', 'KGD/Gdiagdepth.png', 'KGD/Heatmap-G5HWdgm.05.png', 'KGD/MAFHWdgm.05.png', 'KGD/SampDepthHist.png', 'KGD/SNPDepthHist.png'],
         "Demultiplex (text file links)" :  ["TagCount.csv","FastqToTagCount.stdout"],
         "Deduplication" :  ["dedupe_summary.txt"],        
-        "Overall SNP yields" :  ["overall_snp_yield.txt"],
+        "Overall SNP yields" :  ["overall_snp_yield.txt", "information_efficiency.txt"],
         "KGD stdout" :  ["KGD.stdout"],
         "KGD (plots)" : ['KGD/AlleleFreq.png', 'KGD/CallRate.png', 'KGD/Co-call-HWdgm.05.png', 'KGD/Co-call-.png', 'KGD/finplot.png', \
-                         'KGD/GcompareHWdgm.05.png', 'KGD/Gcompare.png', 'KGD/Gdiagdepth.png', 'KGD/G-diag.png', 'KGD/GHWdgm.05diagdepth.png', \
-                         'KGD/GHWdgm.05-diag.png', 'KGD/Heatmap-G5HWdgm.05.png', 'KGD/HWdisMAFsig.png', 'KGD/LRT-hist.png', 'KGD/LRT-QQ.png', \
+                         'KGD/GcompareHWdgm.05.png', 'KGD/Gcompare.png', 'KGD/Gdiagdepth.png', 'KGD/GHWdgm.05diagdepth.png', \
+                         'KGD/InbCompare.png','KGD/Heatmap-G5HWdgm.05.png', 'KGD/HWdisMAFsig.png', \
                          'KGD/MAFHWdgm.05.png', 'KGD/MAF.png', 'KGD/PC1v2G5HWdgm.05.png', 'KGD/SampDepthCR.png', 'KGD/SampDepthHist.png', \
                          'KGD/SampDepth.png', 'KGD/SampDepth-scored.png', 'KGD/SNPCallRate.png', 'KGD/SNPDepthHist.png', 'KGD/SNPDepth.png', \
                          'KGD/X2star-QQ.png', 'KGD/PlateDepth.png', 'KGD/PlateInb.png', 'KGD/SubplateDepth.png', 'KGD/SubplateInb.png'],