diff tools/data_source/ucsc_filter.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/data_source/ucsc_filter.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,68 @@
+# runs after the job (and after the default post-filter)
+from galaxy import datatypes, jobs
+
+def validate(incoming):
+    """Validator"""
+    #raise Exception, 'not quite right'
+    pass
+
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
+    """Sets the name of the data"""
+    outputType = param_dict.get( 'hgta_outputType', None )
+    if isinstance(outputType, list) and len(outputType)>0: outputType = outputType[-1]
+    items = out_data.items()
+    
+    for name, data in items:
+        data.name  = param_dict.get('display', data.name)
+        data.dbkey = param_dict.get('dbkey', '???')
+
+        if outputType == 'wigData':
+            ext = "wig"
+        elif outputType == 'maf':
+            ext = "maf"
+        elif outputType == 'gff':
+            ext = "gff"
+        elif outputType == 'gff3':
+            ext = "gff3"
+        else:
+            if 'hgta_doPrintSelectedFields' in param_dict:
+                ext = "interval"
+            elif 'hgta_doGetBed' in param_dict:
+                ext = "bed"
+            elif 'hgta_doGenomicDna' in param_dict:
+                ext = "fasta"
+            elif 'hgta_doGenePredSequence' in param_dict:
+                ext = "fasta"
+            else:
+                ext = "interval"
+        
+        data = app.datatypes_registry.change_datatype(data, ext)
+        out_data[name] = data
+        
+def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
+    """Verifies the data after the run"""
+    items = out_data.items()
+    for name, data in items:
+        data.set_size()
+        try:            
+            err_msg, err_flag = 'Errors:', False
+            line_count = 0
+            num_lines = len(file(data.file_name).readlines())
+            for line in file(data.file_name):
+                line_count += 1
+                if line and line[0] == '-':
+                    if line_count + 3 == num_lines and not err_flag:
+                        err_flag = True
+                        err_msg = "Warning: It appears that your results have been truncated by UCSC. View the bottom of your result file for details."
+                        break
+                    err_flag = True
+                    err_msg = err_msg +" (line "+str(line_count)+")"+line
+            data.set_peek()
+            if isinstance(data.datatype, datatypes.interval.Interval) and data.missing_meta():
+                data = app.datatypes_registry.change_datatype(data, 'tabular')
+                out_data[name] = data
+            if err_flag:
+                raise Exception(err_msg)
+        except Exception, exc:
+            data.info  = data.info + "\n" + str(exc)
+            data.blurb = "error"