diff dexseq/dexseq_helper.py @ 0:7604d324c5aa draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dexseq/dexseq_helper.py	Fri Aug 28 08:37:31 2015 -0400
@@ -0,0 +1,98 @@
+
+from galaxy.tools.parameters import DataToolParameter
+
+def get_matrix_header( input_dataset ):
+    """
+        Not used currently, because the reload of the ckeckboxes did not work.
+    """
+    input_handle = open( input_dataset.file_name )
+    first_header = input_handle.readline()
+    second_header = input_handle.readline()
+    return [('%s::%s' % (cname2,cname1), str(int(col_num) + 1), False) for col_num, (cname2, cname1) in enumerate(zip(second_header.split()[1:],first_header.split()[1:])) ]
+
+
+
+def _construct_error_map( error_map, rep_dict, rep_parent, child, error_value ):
+    """
+        Its no so easy to create a propper error_map for repetitions in Galaxy.
+        This is a helper function.
+    """
+
+    error_map[ rep_parent ] = [ dict() for t in rep_dict ]
+    for i in range( len( rep_dict ) ):
+        error_map[ rep_parent ][i][ child ] = error_value
+
+
+
+def validate_input( trans, error_map, param_values, page_param_map ):
+    """
+        Validates the user input, before execution.
+    """
+    factors = param_values['rep_factorName']
+    factor_name_list = []
+    factor_duplication = False
+    level_duplication = False
+    overlapping_selection = False
+
+    first_condition = True
+    factor_indieces = list()
+
+    for factor in factors:
+        # factor names should be unique
+        fn = factor['factorName']
+        if fn in factor_name_list:
+            factor_duplication = True
+            break
+        factor_name_list.append( fn )
+
+        level_name_list = list()
+        factor_index_list = list()
+
+        if first_condition and len( factor['rep_factorLevel'] ) < 2:
+            # first condition needs to have at least 2 levels
+            _construct_error_map( error_map, factors, 'rep_factorName', 'rep_factorLevel', [ {'factorLevel': 'The first condition should have at least 2 factor'} for t in factor['rep_factorLevel'] ] )
+
+        for level in factor['rep_factorLevel']:
+            # level names under one factor should be unique
+            fl = level['factorLevel']
+            if fl in level_name_list:
+                level_duplication = True
+            level_name_list.append( fl )
+
+            fi = level['factorIndex']
+            if fi:
+                # the checkboxes should not have an overlap
+                for check in fi:
+                    if check in factor_index_list:
+                        overlapping_selection = True
+                    factor_index_list.append( check )
+
+            print set(factor_index_list)
+            print factor_indieces
+            if set(factor_index_list) in factor_indieces:
+                _construct_error_map( error_map, factors, 'rep_factorName', 'rep_factorLevel', [ {'factorLevel': 'It is not allowed to have two identical factors, that means two factors with the same toggeled checked boxes. '} for t in factor['rep_factorLevel'] ] )
+            else:
+                factor_indieces.append( set(factor_index_list) )
+
+
+
+        if level_duplication:
+            error_map['rep_factorName'] = [ dict() for t in factors ]
+            for i in range( len( factors ) ):
+                error_map['rep_factorName'][i]['rep_factorLevel'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in factor['rep_factorLevel'] ]
+            break
+        if overlapping_selection:
+            error_map['rep_factorName'] = [ dict() for t in factors ]
+            for i in range( len( factors ) ):
+                error_map['rep_factorName'][i]['rep_factorLevel'] = [ {'factorIndex': 'The samples from different factors are not allowed to overlap'} for t in factor['rep_factorLevel'] ]
+            break
+
+        first_condition = False
+
+    if factor_duplication:
+        _construct_error_map( error_map, factors, 'rep_factorName', 'factorName', 'Factor names need to be unique' )
+        """
+        error_map['rep_factorName'] = [ dict() for t in factors ]
+        for i in range( len( factors ) ):
+            error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique'
+        """