Fixed floats in phenotype importer.

Added PrintFunction for debug-printing.
Added PhenotypeImportFunction to AffyWorkflow.

test/workflows/affy_workflowtest.py

@@ -20,13 +20,13 @@ CEL
     def testFloatData(self):
         cel_data = """\
 CEL\tage
-02-05-33\t8
+02-05-33\t8.5
 03-07-38\t9
 """
         dataset = PhenotypeDataset(cel_data)
         self.assertEquals(['CEL', 'phenotypes'], dataset.get_dim_names())
         self.assertEquals(['age'], dataset.get_identifiers('phenotypes'))
-        self.assertEquals([[8],
+        self.assertEquals([[8.5],
                            [9]], dataset.asarray().tolist())
 
     def testCategoryData(self):

workflows/affy_workflow.py

@@ -14,18 +14,31 @@ class AffyWorkflow (workflow.Workflow):
 
         load = workflow.Stage('load', 'Load Data')
         load.add_function(CelFileImportFunction())
+        load.add_function(PhenotypeImportFunction())
         load.add_function(TestDataFunction())
         load.add_function(DatasetLoadFunction())
         self.add_stage(load)
 
         explore = workflow.Stage('explore', 'Explorative analysis')
         explore.add_function(PCAFunction(self))
+        explore.add_function(PrintFunction())
         self.add_stage(explore)
 
         save = workflow.Stage('save', 'Save Data')
         save.add_function(DatasetSaveFunction())
         self.add_stage(save)
 
+class PrintFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'printer', 'Print Stuff')
+
+    def run(self, data):
+        dim1, dim2 = data.get_dim_names()
+        print dim1, dim2
+        print "\t", "\t".join(data.get_identifiers(dim2))
+        for row in zip(data.get_identifiers(dim1), data.asarray().tolist()):
+            print "\t".join(map(str, row))
+        
 
 class TestDataFunction(workflow.Function):  
     def __init__(self):
@@ -146,6 +159,30 @@ class CelFileImportFunction(workflow.Function):
             chooser.destroy()
 
 
+class PhenotypeImportFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'import_phenotype', 'Import Phenotypes')
+
+    def run(self):
+        chooser = gtk.FileChooserDialog(title="Select cel files...", parent=None,
+                                        action=gtk.FILE_CHOOSER_ACTION_OPEN,
+                                        buttons=(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
+                                                 gtk.STOCK_OPEN, gtk.RESPONSE_OK))
+        all_filter = gtk.FileFilter()
+        all_filter.set_name("Tab separated file (*.*)")
+        all_filter.add_pattern("*")
+        chooser.add_filter(all_filter)
+
+        try:
+            if chooser.run() == gtk.RESPONSE_OK:
+                text = open(chooser.get_filename()).read()
+                data = PhenotypeDataset(text)
+                return [data]
+                
+        finally:
+            chooser.destroy()
+        
+
 class PCAFunction(workflow.Function):
     """Generic PCA function."""
     def __init__(self, wf):
@@ -197,7 +234,7 @@ class PhenotypeDataset(dataset.Dataset):
 
         for col_name, column in zip(col_names, columns[1:]):
             try:
-                categories[col_name] = map(int, column)
+                categories[col_name] = map(float, column)
                 phenotypes.append(col_name)
             except ValueError:
                 # category-data
@@ -230,7 +267,7 @@ class PhenotypeDataset(dataset.Dataset):
 
         dataset.Dataset.__init__(self, a, identifiers=[('CEL', cel_names),
                                                        ('phenotypes', phenotypes)],
-                                 shape=(len(cel_names),len(phenotypes)))
+                                 shape=(len(cel_names),len(phenotypes)), name="Phenotype Data")
             
 
     def get_phenotype_table(self):