Mercurial > repos > pavanvidem > dexseq
view dexseq/dexseq_helper.py @ 0:7604d324c5aa draft
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author | pavanvidem |
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date | Fri, 28 Aug 2015 08:37:31 -0400 |
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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' """