From c55a39f7f91bb03e0cf45af72f1b41a1c738b690 Mon Sep 17 00:00:00 2001
From: einarr <einarr@pvv.ntnu.no>
Date: Mon, 17 Apr 2006 20:29:29 +0000
Subject: [PATCH]  * workflows/go_workflow.py: A workflow that makes distance
 matrices based    on gene ontology information. Currently only reads gene
 annotations.

---
 workflows/go_workflow.py | 63 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 workflows/go_workflow.py

diff --git a/workflows/go_workflow.py b/workflows/go_workflow.py
new file mode 100644
index 0000000..0808202
--- /dev/null
+++ b/workflows/go_workflow.py
@@ -0,0 +1,63 @@
+import gtk
+import logger
+from annotations import Annotations
+from workflow import *
+
+class EinarsWorkflow (Workflow):
+
+    def __init__(self, app):
+        Workflow.__init__(self, app)
+        self.name = 'Einar\'s Workflow'
+
+        load = Stage('load', 'Load Data')
+        load.add_function(Function('load', 'Load Microarrays'))
+        self.add_stage(load)
+
+        preproc = Stage('preprocess', 'Preprocessing')
+        preproc.add_function(Function('rma', 'RMA'))
+        self.add_stage(preproc)
+
+        go = Stage('go', 'Gene Ontology Data')
+        go.add_function(LoadAnnotationsFunction())
+        go.add_function(Function('godist', 'GO Distances'))
+        self.add_stage(go)
+
+        regression = Stage('regression', 'Regression')
+        regression.add_function(Function('pls', 'PLS'))
+        self.add_stage(regression)
+        
+        logger.log('debug', '\tEinar\'s workflow is now active')
+
+class LoadAnnotationsFunction(Function):
+
+    def __init__(self):
+        Function.__init__(self, 'load-go-ann', 'Load Annotations')
+        self.annotations = None
+
+    def load_file(self, filename):
+        f = open(filename)
+        self.annotations = Annotations('genes', 'go-terms')
+
+        for line in f.readlines():
+            val = line.split(' \t')
+
+            if len(val) > 1:
+                val = [v.strip() for v in val]
+                retval.add_annotations('genes', val[0], 
+                                       'go-terms', set(val[1:]))
+            
+    def on_response(self, dialog, response):
+        if response == gtk.RESPONSE_OK:
+            logger.log('notice', 'Reading file: %s' % dialog.get_filename())
+            self.load_file(dialog.get_filename())
+
+    def run(self, data):
+        btns = ('Open', gtk.RESPONSE_OK, \
+                'Cancel', gtk.RESPONSE_CANCEL)
+        dialog = gtk.FileChooserDialog('Open GO Annotation File',
+                                       buttons=btns)
+        dialog.connect('response', self.on_response)
+        dialog.run()
+        dialog.destroy()
+        return [self.annotations]
+