gff3/gff3.py
def check_phase(self):
        """
        1. get a list of CDS with the same parent
        2. sort according to strand
        3. calculate and validate phase
        """
        plus_minus = set(['+', '-'])
        for k, g in groupby(sorted([line for line in self.lines if  line['line_type'] == 'feature' and line['type'] == 'CDS' and 'Parent' in line['attributes']], key=lambda x: x['attributes']['Parent']), key=lambda x: x['attributes']['Parent']):
            cds_list = list(g)
            strand_set = list(set([line['strand'] for line in cds_list]))
            if len(strand_set) != 1:
                for line in cds_list:
                    self.add_line_error(line, {'message': 'Inconsistent CDS strand with parent: {0:s}'.format(k), 'error_type': 'STRAND'})
                continue
            if len(cds_list) == 1:
                if cds_list[0]['phase'] != 0:
                    self.add_line_error(cds_list[0], {'message': 'Wrong phase {0:d}, should be {1:d}'.format(cds_list[0]['phase'], 0), 'error_type': 'PHASE'})
                continue
            strand = strand_set[0]
            if strand not in plus_minus:
                # don't process unknown strands
                continue
            if strand == '-':
                # sort end descending
                sorted_cds_list = sorted(cds_list, key=lambda x: x['end'], reverse=True)
            else:
                sorted_cds_list = sorted(cds_list, key=lambda x: x['start'])
            phase = 0
            for line in sorted_cds_list:
                if line['phase'] != phase:
                    self.add_line_error(line, {'message': 'Wrong phase {0:d}, should be {1:d}'.format(line['phase'], phase), 'error_type': 'PHASE'})
                phase = (3 - ((line['end'] - line['start'] + 1 - phase) % 3)) % 3
def check_phase(self):
        """
        1. get a list of CDS with the same parent
        2. sort according to strand
        3. calculate and validate phase
        """
        plus_minus = set(['+', '-'])
        for k, g in groupby(sorted([line for line in self.lines if  line['line_type'] == 'feature' and line['type'] == 'CDS' and 'Parent' in line['attributes']], key=lambda x: x['attributes']['Parent']), key=lambda x: x['attributes']['Parent']):
            cds_list = list(g)
            strand_set = list(set([line['strand'] for line in cds_list]))
            if len(strand_set) != 1:
                for line in cds_list:
                    self.add_line_error(line, {'message': 'Inconsistent CDS strand with parent: {0:s}'.format(k), 'error_type': 'STRAND'})
                continue
            if len(cds_list) == 1:
                if cds_list[0]['phase'] != 0:
                    self.add_line_error(cds_list[0], {'message': 'Wrong phase {0:d}, should be {1:d}'.format(cds_list[0]['phase'], 0), 'error_type': 'PHASE'})
                continue
            strand = strand_set[0]
            if strand not in plus_minus:
                # don't process unknown strands
                continue
            if strand == '-':
                # sort end descending
                sorted_cds_list = sorted(cds_list, key=lambda x: x['end'], reverse=True)
            else:
                sorted_cds_list = sorted(cds_list, key=lambda x: x['start'])
            phase = 0
            for line in sorted_cds_list:
                if line['phase'] != phase:
                    self.add_line_error(line, {'message': 'Wrong phase {0:d}, should be {1:d}'.format(line['phase'], phase), 'error_type': 'PHASE'})
                phase = (3 - ((line['end'] - line['start'] + 1 - phase) % 3)) % 3
def check_phase ( self ) : plus_minus = set ( [ '+' , '-' ] ) for k , g in groupby ( sorted ( [ line for line in self . lines if line [ 'line_type' ] == 'feature' and line [ 'type' ] == 'CDS' and 'Parent' in line [ 'attributes' ] ] , key = lambda x : x [ 'attributes' ] [ 'Parent' ] ) , key = lambda x : x [ 'attributes' ] [ 'Parent' ] ) : cds_list = list ( g ) strand_set = list ( set ( [ line [ 'strand' ] for line in cds_list ] ) ) if len ( strand_set ) != 1 : for line in cds_list : self . add_line_error ( line , { 'message' : 'Inconsistent CDS strand with parent: {0:s}' . format ( k ) , 'error_type' : 'STRAND' } ) continue if len ( cds_list ) == 1 : if cds_list [ 0 ] [ 'phase' ] != 0 : self . add_line_error ( cds_list [ 0 ] , { 'message' : 'Wrong phase {0:d}, should be {1:d}' . format ( cds_list [ 0 ] [ 'phase' ] , 0 ) , 'error_type' : 'PHASE' } ) continue strand = strand_set [ 0 ] if strand not in plus_minus : # don't process unknown strands continue if strand == '-' : # sort end descending sorted_cds_list = sorted ( cds_list , key = lambda x : x [ 'end' ] , reverse = True ) else : sorted_cds_list = sorted ( cds_list , key = lambda x : x [ 'start' ] ) phase = 0 for line in sorted_cds_list : if line [ 'phase' ] != phase : self . add_line_error ( line , { 'message' : 'Wrong phase {0:d}, should be {1:d}' . format ( line [ 'phase' ] , phase ) , 'error_type' : 'PHASE' } ) phase = ( 3 - ( ( line [ 'end' ] - line [ 'start' ] + 1 - phase ) % 3 ) ) % 3
1. get a list of CDS with the same parent
        2. sort according to strand
        3. calculate and validate phase
1 . get a list of CDS with the same parent 2 . sort according to strand 3 . calculate and validate phase