diff tools/maf/maf_to_bed_code.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_to_bed_code.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,59 @@
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.align import maf
+from galaxy import datatypes, config, jobs 
+from shutil import move
+
+def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
+    output_data = out_data.items()[0][1]
+    history = output_data.history
+    if history == None:
+        print "unknown history!"
+        return
+    new_stdout = ""
+    split_stdout = stdout.split("\n")
+    basic_name = output_data.name
+    output_data_list = []
+    for line in split_stdout:
+        if line.startswith("#FILE1"):
+            fields = line.split("\t")
+            dbkey = fields[1]
+            filepath = fields[2]
+            output_data.dbkey = dbkey
+            output_data.name = basic_name + " (" + dbkey + ")"
+            app.model.context.add( output_data )
+            app.model.context.flush()
+            output_data_list.append(output_data)
+        elif line.startswith("#FILE"):
+            fields = line.split("\t")
+            dbkey = fields[1]
+            filepath = fields[2]
+            newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context )
+            newdata.set_size()
+            newdata.extension = "bed"
+            newdata.name = basic_name + " (" + dbkey + ")"
+            app.model.context.add( newdata )
+            app.model.context.flush()
+            history.add_dataset( newdata )
+            app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset )
+            app.model.context.add( history )
+            app.model.context.flush()
+            try:
+                move(filepath,newdata.file_name)
+                newdata.info = newdata.name
+                newdata.state = newdata.states.OK
+            except:
+                newdata.info = "The requested file is missing from the system."
+                newdata.state = newdata.states.ERROR
+            newdata.dbkey = dbkey
+            newdata.init_meta()
+            newdata.set_meta()
+            newdata.set_peek()
+            app.model.context.flush()
+            output_data_list.append(newdata)
+        else:
+            new_stdout = new_stdout + line
+        for data in output_data_list:
+            if data.state == data.states.OK:
+                data.info = new_stdout
+                app.model.context.add( data )
+                app.model.context.flush()