2.1.3 4/26/19

AltAnalyze.py

@@ -6276,6 +6276,7 @@ def commandLineRun():
     PearsonThreshold = 0.1
     returnCentroids = 'community'
     runCompleteWorkflow=True
+    referenceFull=None
     k=None
     labels=None
 
@@ -6343,7 +6344,7 @@ def commandLineRun():
                                                          'correlationCutoff=','referenceType=','DE=','cellHarmonyMerge=',
                                                          'o=','dynamicCorrelation=','runCompleteWorkflow=','adjp=',
                                                          'fold=','performDiffExp=','centerMethod=', 'k=','bamdir=',
-                                                         'downsample=','query='])
+                                                         'downsample=','query=','referenceFull='])
     except Exception:
         print traceback.format_exc()
         print "There is an error in the supplied command-line arguments (each flag requires an argument)"; sys.exit()
@@ -8049,6 +8050,7 @@ def commandLineRun():
                     elif opt == '--centerMethod': CenterMethod = arg
                     elif opt == '--labels': labels = arg
                     elif opt == '--genes': genes = arg
+                    elif opt == '--referenceFull': referenceFull = arg
                 fl = UI.ExpressionFileLocationData('','','','')
                 fl.setSpecies(species)
                 fl.setVendor(manufacturer)
@@ -8087,10 +8089,12 @@ def commandLineRun():
                 if len(genes)>0 and ('h5' in custom_reference or 'mtx' in custom_reference):
                     fl.set_reference_exp_file(custom_reference)
                     custom_reference = genes
+                if referenceFull != None:
+                    fl.set_reference_exp_file(referenceFull)
 
                 UI.remoteLP(fl, expr_input_dir, manufacturer, custom_reference, geneModel, None, modelSize=modelSize, CenterMethod=CenterMethod) #,display=display
                 #graphic_links = ExpressionBuilder.remoteLineageProfiler(fl,input_file_dir,array_type,species,manufacturer)
-                print_out = 'Lineage profiles and images saved to the folder "DataPlots" in the input file folder.'
+                print_out = 'Alignments and images saved to the folder "DataPlots" in the input file folder.'
                 print print_out
             except Exception:
                 print traceback.format_exc() 

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","/Users/saljh8/Desktop/DemoData/ICGS-Mm","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","/Volumes/salomonis2/HCA-Immune-10x-data/Bone-Marrow/MantonBM5/cellHarmony/heatmaps","all"
+"PathFile","local","/Users/saljh8/Desktop/DemoData/ICGS-Mm","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/options.txt

@@ -120,10 +120,11 @@ pca_algorithm	Algorithm to use	comboBox	PCA			SVD	SVD|Eigen Vectors|t-SNE|UMAP	S
 dimensions	Dimensions to display	comboBox	PCA			3D	2D|3D	2D|3D	2D|3D	2D|3D	2D|3D	2D|3D	2D|3D
 colorByGene	(Optional) Enter a gene to color the PCA by	enter	PCA				---	---	---	---	---	---	---
 pcaGeneSets	(Optional) Store top 200 component genes as	enter	PCA				---	---	---	---	---	---	---
-input_lineage_file	"Select an expression file to be aligned (txt, mtx or h5)"	file	LineageProfiler	Recommended: Select an un-filtered log2 expression file (query)			---	---	---	---	---	---	---
 classificationAnalysis	Analysis to perform	comboBox	LineageProfiler			cellHarmony	cellHarmony|LineageProfiler	cellHarmony|LineageProfiler	cellHarmony|LineageProfiler	cellHarmony|LineageProfiler	cellHarmony|LineageProfiler	cellHarmony|LineageProfiler	cellHarmony|LineageProfiler
-markerFinder_file	Select an ICGS or MarkerFinder clusters file	file	LineageProfiler	Recommended: Any heatmap text output file from AltAnalyze (reference)			---	---	---	---	---	---	---
-labels	(optional) Supply a reference cell annotation file	file	LineageProfiler				---	---	---	---	---	---	---
+markerFinder_file	Select Reference File	file	LineageProfiler	ICGS or MarkerFinder formatted clustered expression txt file			---	---	---	---	---	---	---
+referenceFull	(optional) Full Reference Expression File	file	LineageProfiler	"Un-filtered expression file (txt, mtx or h5)"			---	---	---	---	---	---	---
+labels	(optional) Reference Cell Annotation File	file	LineageProfiler	Cell-to-groups annotation/labels txt file for the reference			---	---	---	---	---	---	---
+input_lineage_file	Select Query File	file	LineageProfiler	"Un-filtered expression file (txt, mtx or h5)"			---	---	---	---	---	---	---
 performDiffExp	Perform differential expression analysis	comboBox	LineageProfiler			yes	yes|no	yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
 returnCentroids	Align to cluster centroid instead of cell	comboBox	LineageProfiler			community	community|centroid|cell	community|centroid|cell	community|centroid|cell	community|centroid|cell	community|centroid|cell	community|centroid|cell	community|centroid|cell
 PearsonThreshold	Enter cellHarmony Pearson correlation threshold	enter	LineageProfiler			0.4	---	---	---	---	---	---	---

Config/version.txt

@@ -1 +1 @@
-EnsMart72	04/24/2019
+EnsMart72	04/26/2019