12/3/2019

AltAnalyze.py

@@ -6347,7 +6347,8 @@ def commandLineRun():
                                                          'correlationCutoff=','referenceType=','DE=','cellHarmonyMerge=',
                                                          'o=','dynamicCorrelation=','runCompleteWorkflow=','adjp=',
                                                          'fold=','performDiffExp=','centerMethod=', 'k=','bamdir=',
-                                                         'downsample=','query=','referenceFull=', 'maskGroups='])
+                                                         'downsample=','query=','referenceFull=', 'maskGroups=',
+                                                         'elite_dir='])
     except Exception:
         print traceback.format_exc()
         print "There is an error in the supplied command-line arguments (each flag requires an argument)"; sys.exit()
@@ -6533,6 +6534,15 @@ def commandLineRun():
 
     ######## Perform analyses independent from AltAnalyze database centric analyses that require additional parameters
     if len(image_export) > 0 or len(accessoryAnalysis)>0 or runICGS:
+        """ Annotate existing ICGS groups with selected GO-Elite results """
+        if 'annotateICGS' in accessoryAnalysis:
+            for opt, arg in options: ### Accept user input for these hierarchical clustering variables
+                if opt == '--elite_dir':
+                    goelite_path = arg
+            import RNASeq
+            RNASeq.predictCellTypesFromClusters(groups_file, goelite_path)
+            sys.exit()
+
         if runICGS:
             #python AltAnalyze.py --runICGS yes --platform "RNASeq" --species Hs --column_method hopach --column_metric euclidean --rho 0.3 --ExpressionCutoff 1 --FoldDiff 4 --SamplesDiffering 3 --restrictBy protein_coding --excludeCellCycle conservative --removeOutliers yes --expdir /RNA-Seq/run1891_normalized.txt
             #python AltAnalyze.py --runICGS yes --expdir "/Users/saljh8/Desktop/demo/Myoblast/ExpressionInput/exp.myoblast.txt" --platform "3'array" --species Hs --GeneSetSelection BioMarkers --PathwaySelection Heart --column_method hopach --rho 0.4 --ExpressionCutoff 200 --justShowTheseIDs "NKX2-5 T TBX5" --FoldDiff 10 --SamplesDiffering 3 --excludeCellCycle conservative
@@ -8630,8 +8640,8 @@ def versionCheck():
         if use_Tkinter == 'yes':
             AltAnalyzeSetup(skip_intro)
     except:
-        print traceback.format_exc()
-        pass
+        if 'SystemExit' not in traceback.format_exc():
+            print traceback.format_exc()
 
     """ To do list:
     3) SQLite for gene-set databases prior to clustering and network visualization

Config/default-files.csv

@@ -3,11 +3,11 @@
 "exon_seq","","HuEx-1_0-st-v2.hg16.probeset.fa","Hs"
 "exon_seq","","MoEx-1_0-st-v1.mm5.probeset.fa","Mm"
 "exon_seq","","RaEx-1_0-st-v1.rn3.probeset.fa","Rn"
-"PathDir","local","/Users/saljh8/Downloads","all"
+"PathDir","local","/Volumes/salomonis2/CCHMC-Collaborations/Claire_chougnet-10X-Rhesus/ScSeq-2019/Merged/MergedFiles-Rhesus-wo-outliers/MergedFiles-Rhesus/ICGS-NMF_euclidean_cc","all"
 "temp","temp","ftp://ftp.geneontology.org/pub/go/ontology-archive/function.ontology.2008-08-01.gz","all"
 "Program/Download","Status","Location","Species"
 "url","url","http://altanalyze.org/archiveDBs/","all"
-"PathFile","local","/Users/saljh8/Documents/1-manuscripts/David/R412X/completed/cellHarmony/query/R412X-het/cellHarmony/OtherFiles","all"
+"PathFile","local","","all"
 "TrEMBL","ftp","ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_human.dat.gz","Hs"
 "TrEMBL","ftp","ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_rodents.dat.gz","Mm|Rn"
 "APT","local","AltDatabase/affymetrix/APT","all"

Config/version.txt

@@ -1 +1 @@
-EnsMart72	11/25/2019
+EnsMart72	12/03/2019

GO_Elite.py

@@ -2251,7 +2251,7 @@ def commandLineRun():
             if wpid==None:
                 print 'Please provide a valid WikiPathways ID (e.g., WP1234)';sys.exit()
             if species_code==None:
-                print 'Please provide a valid species ID for an installed database (to install: --update Official --species Hs --version EnsMart62Plus)';sys.exit()
+                print 'Please provide a valid species ID for an installed database (to install: --update Official --species Hs --version EnsMart91Plus)';sys.exit()
             if criterion_input_folder==None:
                 print 'Please provide a valid file location for your input IDs (also needs to inlcude system code and value column)';sys.exit()
             from visualization_scripts import WikiPathways_webservice

UI.py

@@ -2544,11 +2544,8 @@ def runPredictGroupsTest():
                 button_instance = Button(self._parent, text='Kallisto License', command=self.openPDFHelp)
                 button_instance.pack(side = 'left', padx = 5, pady = 5)
 
-            try:
-                self._parent.protocol("WM_DELETE_WINDOW", self.deleteWindow)
-                self._parent.mainloop()
-            except:
-                pass
+            self._parent.protocol("WM_DELETE_WINDOW", self.deleteWindow)
+            self._parent.mainloop()
 
     def verifyExpressionFile(self):
         continue_analysis = False ### See if the input file is already present
@@ -4026,8 +4023,7 @@ def __init__(self,message,button_text):
         Label(parent, text='\n'+self.message+'\n'+nulls).pack()  
         quit_button = Button(parent, text='Quit', command=self.quit); quit_button.pack(side = 'bottom', padx = 5, pady = 5)
         text_button = Button(parent, text=self.button_text, command=parent.destroy); text_button.pack(side = 'bottom', padx = 5, pady = 5)
-        try: parent.mainloop()
-        except: pass
+        parent.mainloop()
     def quit(self):
         try: self._parent.quit(); self._parent.destroy(); sys.exit()
         except Exception: self._parent.quit(); sys.exit()
@@ -5557,8 +5553,7 @@ def rebootAltAnalyzeGUI(selected_parameters,user_variables):
                         IndicatorWindow(print_out,'Continue')
 
             if additional_analyses == 'Hierarchical Clustering':
-                print 'Hierarchical Clustering'
-
+                print 'Performing Hierarchical Clustering'
                 selected_parameters.append('Hierarchical Clustering')
 
                 supported_geneset_types = getSupportedGeneSetTypes(species,'gene-mapp')

stats_scripts/metaDataAnalysis.py

@@ -408,7 +408,7 @@ def performDifferentialExpressionAnalysis(species,platform,input_file,groups_db,
                         initial_filtered.append(values[x])
                     filtered_values=[]
                     for x in initial_filtered:
-                        if x != '':
+                        if x != '' and x!= 'NA':
                             filtered_values.append(float(x))
                         unfiltered.append(x)
                     #if uid == 'ENSG00000105321:E3.2-E4.2 ENSG00000105321:E2.3-E4.2' and 'inner cell mass' in group:

unique.py

@@ -108,10 +108,15 @@ def filepath(filename,force=None):
     import export
     parent_dir = export.findParentDir(filename)
     actual_file = export.findFilename(filename)
-    if os.path.isdir(dir+'/'+parent_dir):
+    try:
+        #if os.path.exists(dir+'/'+parent_dir):
+        dir_list = os.listdir(dir+'/'+parent_dir)
         fn = dir+'/'+parent_dir+'/'+actual_file
-        return fn
-
+        if '.txt' in fn or '.log' in fn:
+            return fn
+    except:
+        pass
+
     if filename== '':  ### Windows will actually recognize '' as the AltAnalyze root in certain situations but not others
         fn = dir
     elif ':' in filename:

visualization_scripts/clustering.py

@@ -1433,19 +1433,18 @@ def exportFlatClusterData(filename, root_dir, dataset_name, new_row_header,new_c
 
     ### Export GO-Elite input files
     allGenes={}
+    sc=sy
     for cluster in cluster_db:
         export_elite = export.ExportFile(elite_dir + '/' + cluster + '.txt')
         if sy == None:
             export_elite.write('ID\n')
         else:
             export_elite.write('ID\tSystemCode\n')
         for id in cluster_db[cluster]:
-            try:
-                i1, i2 = string.split(id, ' ')
-                if i1 == i2:
-                    id = i1
-            except Exception:
-                pass
+            if ' ' in id:
+                ids = string.split(id, ' ')
+                if ids[0] == ids[1]:
+                    id = ids[0]
             else:
                 if sy == '$En:Sy':
                     id = string.split(id, ':')[1]
@@ -7744,7 +7743,36 @@ def importCellHarmonyPseudoBulkFolds(filename):
     eo1.close()
     eo2.close()
 
+def exportSeuratMarkersToClusters(filename):
+    prior_cluster = None
+    for line in open(filename, 'rU').xreadlines():
+        data = cleanUpLine(line)
+        cluster,gene = string.split(data, '\t')
+        if cluster!= prior_cluster:
+            try: eo.close()
+            except: pass
+            path = filename[:-4]+'_'+cluster+'.txt'
+            eo = export.ExportFile(path)
+            eo.write('UID\tSy\n')
+        eo.write(gene+'\tSy\n')
+        prior_cluster = cluster
+    eo.close()
+
+def tempFunction(filename):
+    path = filename[:-4]+'_cleaned'+'.txt'
+    eo = export.ExportFile(path)
+    for line in open(filename, 'rU').xreadlines():
+        data = cleanUpLine(line)
+        t = string.split(data, '\t')
+        eo.write(string.join(t[1:],'\t')+'\n')
+    eo.close()
+
 if __name__ == '__main__':
+    tempFunction('/Users/saljh8/Downloads/LungCarcinoma/HCC.S5063.TPM.txt');sys.exit()
+    a = '/Users/saljh8/Desktop/dataAnalysis/SalomonisLab/Leucegene/July-2017/PSI/SpliceICGS.R1.Depleted.12.27.17/all-depleted-and-KD/StatisticalEnrichment-MNBL1'
+    compareEventLists(a);sys.exit()
+    filename = '/Users/saljh8/Downloads/Kerscher_lists_mouse_versus_mouse_and_human_gene_lists/Top50MouseandHuman1-clusters.txt'
+    #exportSeuratMarkersToClusters(filename); sys.exit()
     organized_diff_ref = '/Volumes/salomonis2/Grimes/RNA/scRNA-Seq/10x-Genomics/WuXi-David-Nature-Revision/PROJ-00584/fastqs/DM-4-Gfi1-R412X-ModGMP-1694-ADT/outs/filtered_gene_bc_matrices/Merged-Cells/centroid-revised/custom/cellHarmony/OrganizedDifferentials.txt'
     repair1_folds = '/Volumes/salomonis2/Grimes/RNA/scRNA-Seq/10x-Genomics/WuXi-David-Nature-Revision/PROJ-00584/fastqs/DM-5-Gfi1-R412X-R412X-ModGMP-1362-ADT/outs/filtered_gene_bc_matrices/Merged-Cells/hybrid/cellHarmony-vs-DM2-1.2-fold-adjp/OtherFiles/exp.ICGS-cellHarmony-reference__DM-5-Gfi1-R412X-R412X-ModGMP-1362-D7Cells-ADT-Merged_matrix_CPTT-AllCells-folds.txt'
     repair2_folds = '/Volumes/salomonis2/Grimes/RNA/scRNA-Seq/10x-Genomics/WuXi-David-Nature-Revision/PROJ-00584/fastqs/DM-6-Gfi1-R412X-Irf8-ModGMP-1499-ADT/outs/filtered_gene_bc_matrices/Merged-Cells-iseq/cellHarmony-centroid-revsied/hybrid/cellHarmony/OtherFiles/exp.ICGS-cellHarmony-reference__DM-6-Gfi1-R412X-Irf8-ModGMP-1499-ADT_matrix-3_matrix_CPTT-hybrid-AllCells-folds.txt'
@@ -7771,11 +7799,11 @@ def importCellHarmonyPseudoBulkFolds(filename):
     TF_file = '/Users/saljh8/Desktop/dataAnalysis/SalomonisLab/NCI-R01/CCSB_TFIso_Clones.txt'
     PSI_dir = '/Volumes/salomonis2/NCI-R01/TCGA-BREAST-CANCER/TCGA-files-Ens91/bams/AltResults/AlternativeOutput/OncoSPlice-All-Samples-filtered-names/SubtypeAnalyses-Results/round1/Events-dPSI_0.1_adjp/'
     #convertPSICoordinatesToBED(PSI_dir);sys.exit()
-    summarizePSIresults(PSI_dir,TF_file);sys.exit()
+    #summarizePSIresults(PSI_dir,TF_file);sys.exit()
 
     filename = '/Users/saljh8/Desktop/dataAnalysis/SalomonisLab/Anukana/Breast-Cancer/TF-isoform/TF_ratio_correlation-analysis/tcga_rsem_isopct_filtered-filtered.2-filtered.txt'
     TF_file = '/Users/saljh8/Desktop/dataAnalysis/SalomonisLab/Anukana/Breast-Cancer/TF-isoform/Ensembl-isoform-key-CCSB.txt'
-    exportIntraTFIsoformCorrelations(filename,TF_file,0.3,anticorrelation=True);sys.exit()
+    #exportIntraTFIsoformCorrelations(filename,TF_file,0.3,anticorrelation=True);sys.exit()
     input_file= '/Volumes/salomonis2/NCI-R01/TCGA-BREAST-CANCER/Anukana/UO1analysis/xenabrowserFiles/tcga_rsem_isoform_tpm_filtered.txt'
     #convertXenaBrowserIsoformDataToStandardRatios(input_file);sys.exit()
     Mm_Ba_coordinates = '/Users/saljh8/Desktop/dataAnalysis/SalomonisLab/Krithika/Baboon-Mouse/mm10-circadian_liftOverTo_baboon.txt'
@@ -7818,7 +7846,7 @@ def importCellHarmonyPseudoBulkFolds(filename):
     #removeRedundantCluster(a,b);sys.exit()
     a = '/Users/saljh8/Desktop/dataAnalysis/SalomonisLab/Leucegene/July-2017/PSI/SpliceICGS.R1.Depleted.12.27.17/all-depleted-and-KD'
     #a = '/Users/saljh8/Desktop/Ashish/all/Events-dPSI_0.1_rawp-0.01/'
-    compareEventLists(a);sys.exit()
+
     #filterPSIValues('/Users/saljh8/Desktop/dataAnalysis/SalomonisLab/Leucegene/July-2017/PSI/CORNEL-AML/PSI/exp.Cornell-Bulk.txt');sys.exit()
     #compareGenomicLocationAndICGSClusters();sys.exit()
     #ViolinPlot();sys.exit()