Commit 3163f110 authored by Witold Dyrka's avatar Witold Dyrka
Browse files

bugfix to handling full window for sets of sequences with RQAFeatureSet

parent 8b599dbd

quantiprot/metrics/rqa.py

+10 −10
Original line number Diff line number Diff line
@@ -457,33 +457,33 @@ class RQAFeatureSet(object): 
            rec_table = _recurrence_common(seq.data, **self.params)



            if window == 0:

                window = len(seq.data)

                my_window = len(seq.data)



            if 'recurrence' in self.features or \

               'ratio_determinism' in self.features or \

               'ratio_palindromism' in self.features:

                rqa_output['recurrence'] = []

                for win_pos in range(len(seq.data) - window + 1):

                    rec_table_part = rec_table[win_pos:win_pos + window,

                                               win_pos:win_pos + window]

                for win_pos in range(len(seq.data) - my_window + 1):

                    rec_table_part = rec_table[win_pos:win_pos + my_window,

                                               win_pos:win_pos + my_window]

                    rqa_output['recurrence'].append(recurrence([],

                         _rec_table=rec_table_part, **self.params))



            if 'determinism' in self.features or \

               'ratio_determinism' in self.features:

                rqa_output['determinism'] = []

                for win_pos in range(len(seq.data) - window + 1):

                    rec_table_part = rec_table[win_pos:win_pos + window,

                                               win_pos:win_pos + window]

                for win_pos in range(len(seq.data) - my_window + 1):

                    rec_table_part = rec_table[win_pos:win_pos + my_window,

                                               win_pos:win_pos + my_window]

                    rqa_output['determinism'].append(determinism([],

                        _rec_table=rec_table_part, **self.params))



            if 'palindromism' in self.features or \

               'ratio_palindromism' in self.features:

                rqa_output['palindromism'] = []

                for win_pos in range(len(seq.data) - window + 1):

                    rec_table_part = rec_table[win_pos:win_pos + window,

                                               win_pos:win_pos + window]

                for win_pos in range(len(seq.data) - my_window + 1):

                    rec_table_part = rec_table[win_pos:win_pos + my_window,

                                               win_pos:win_pos + my_window]

                    rqa_output['palindromism'].append(palindromism([],

                        _rec_table=rec_table_part, **self.params))