11/25/2019

AltAnalyze.py

@@ -8477,6 +8477,19 @@ def write(self, message):
         self.log.close()
 
     def flush(self): pass
+
+class SysLogger(object):
+    def __init__(self,null): 
+        self.terminal = sys.stdout
+        self.log = open(sys_log_file, "w")
+
+    def write(self, message):
+        self.terminal.write(message)
+        self.log = open(sys_log_file, "a")
+        self.log.write(message)
+        self.log.close()
+
+    def flush(self): pass
 
 def verifyPath(filename):
     ### See if the file is in the current working directory
@@ -8579,31 +8592,51 @@ def unpackConfigFiles():
             zip_ref.extractall(userdir+"/altanalyze")
         print '...written'
 
+def systemLog():
+    global sys_log_file
+    sys_log_file = filepath('Config/report.log')
+    sys_report = open(sys_log_file,'w'); sys_report.close()
+    sys.stdout = SysLogger('')
+
+def versionCheck():
+    import platform
+    if platform.system()=='Darwin':
+        if platform.mac_ver()[0] == '10.14.6':
+            print 'CRITICAL ERROR. AltAanlyze has a critical incompatibility with this specific OS version.'
+            url = 'http://www.altanalyze.org/MacOS-critical-error.html'
+            try: webbrowser.open(url)
+            except Exception: pass
+            sys.exit()
+
 if __name__ == '__main__':
     try: mlp.freeze_support()
     except Exception: pass
-
+
+    systemLog()
+    sys_log_file = filepath('Config/report.log')
+    print 'Using the Config location:',sys_log_file
+
+    versionCheck()
+
     try: unpackConfigFiles()
     except: pass
     #testResultsPanel()
     skip_intro = 'yes'; #sys.exit()
     #skip_intro = 'remoteViewer'
     dependencyCheck()
-    runCommandLineVersion()
-
-    if use_Tkinter == 'yes': AltAnalyzeSetup(skip_intro)
+    try:
+        runCommandLineVersion()
+
+        if use_Tkinter == 'yes':
+            AltAnalyzeSetup(skip_intro)
+    except:
+        print traceback.format_exc()
+        pass
 
     """ To do list:
-    1) RNA-Seq and LineageProfiler: threshold based RPKM expression filtering for binary absent present gene and exon calls
     3) SQLite for gene-set databases prior to clustering and network visualization
-    5) (explored - not good) Optional algorithm type of PCA
     7) (partially) Integrate splicing factor enrichment analysis (separate module?)
-    11) Update fields in summary combined alt.exon files (key by probeset)
-    12) Check field names for junction, exon, RNA-Seq in summary alt.exon report
-    14) Proper FDR p-value for alt.exon analyses (include all computed p-values)
-    15) Add all major clustering and LineageProfiler options to UI along with stats filtering by default
     17) Support R check (and response that they need it) along with GUI gcrma, agilent array, hopach, combat
-    18) Probe-level annotations from Ensembl (partial code in place) and probe-level RMA in R (or possibly APT) - google pgf for U133 array
     19) Update the software from the software
 
     Advantages of this tool kit:
@@ -8620,11 +8653,5 @@ def unpackConfigFiles():
     1) MySQL or equivalent transition for all large database queries (e.g., HuEx 2.1 on-the-fly coordinate mapping).
     3) Isoform-domain network visualization and WP overlays.
     4) Webservice calls to in silico protein translation, domain prediction, splicing factor regulation.
-
-    ### 2.0.9
-    moncole integration
-    generic and cell classification machine learning
-    PCR primer design (gene centric after file selection)
-    BAM->BED (local SAMTools)
-    updated APT
+
     """

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/Dropbox/Collaborations/Hupert/10X-Huppert-JB-20190425-3v3mm/cellHarmony/DifferentialExpression_Fold_1.5_rawp_0.05","all"
+"PathDir","local","/Users/saljh8/Downloads","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/reference","all"
+"PathFile","local","/Users/saljh8/Documents/1-manuscripts/David/R412X/completed/cellHarmony/query/R412X-het/cellHarmony/OtherFiles","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	11/23/2019
+EnsMart72	11/25/2019

UI.py

@@ -2544,8 +2544,11 @@ def runPredictGroupsTest():
                 button_instance = Button(self._parent, text='Kallisto License', command=self.openPDFHelp)
                 button_instance.pack(side = 'left', padx = 5, pady = 5)
 
-            self._parent.protocol("WM_DELETE_WINDOW", self.deleteWindow)
-            self._parent.mainloop()
+            try:
+                self._parent.protocol("WM_DELETE_WINDOW", self.deleteWindow)
+                self._parent.mainloop()
+            except:
+                pass
 
     def verifyExpressionFile(self):
         continue_analysis = False ### See if the input file is already present
@@ -4023,7 +4026,8 @@ 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)
-        parent.mainloop()
+        try: parent.mainloop()
+        except: pass
     def quit(self):
         try: self._parent.quit(); self._parent.destroy(); sys.exit()
         except Exception: self._parent.quit(); sys.exit()
@@ -5553,6 +5557,8 @@ def rebootAltAnalyzeGUI(selected_parameters,user_variables):
                         IndicatorWindow(print_out,'Continue')
 
             if additional_analyses == 'Hierarchical Clustering':
+                print 'Hierarchical Clustering'
+
                 selected_parameters.append('Hierarchical Clustering')
 
                 supported_geneset_types = getSupportedGeneSetTypes(species,'gene-mapp')
@@ -5648,6 +5654,7 @@ def rebootAltAnalyzeGUI(selected_parameters,user_variables):
                         IndicatorWindow(print_out,'Continue')
 
             if additional_analyses == 'Dimensionality Reduction':
+                print 'Performing Dimensionality Reduction'
                 selected_parameters.append('Dimensionality Reduction')
                 status = 'repeat'
                 while status == 'repeat':

import_scripts/mergeFiles.py

@@ -56,22 +56,15 @@ def cleanUpLine(line):
     return data
 
 def combineAllLists(files_to_merge,original_filename,includeColumns=False):
-    headers =[]; all_keys={}; dataset_data={}; files=[]; unique_filenames=[]
-    count=0
+    headers =[]; all_keys={}; dataset_data={}; files=[]
     for filename in files_to_merge:
+        print filename
         duplicates=[]
-        count+=1
-        fn=filepath(filename); x=0; combined_data ={}
+        fn=filepath(filename); x=0; combined_data ={}; files.append(filename)
         if '/' in filename:
             file = string.split(filename,'/')[-1][:-4]
         else:
             file = string.split(filename,'\\')[-1][:-4]
-        ### If two files with the same name being merged
-        if file in unique_filenames:
-            file += str(count)
-        unique_filenames.append(file)
-        print file
-        files.append(filename)
         for line in open(fn,'rU').xreadlines():         
             data = cleanUpLine(line)
             t = string.split(data,'\t')