        self.options.update(self.define_options(['pepfile', 'proteincol'],
                                                prottable_options))

    def parse_input(self, **kwargs):
        super().parse_input(**kwargs)
        self.headertypes = ['probability']

    def initialize_input(self):
        super().initialize_input()
        self.in_peptides = reader.generate_tsv_peptides(self.pepfile)
        pepheader = reader.get_tsv_header(self.pepfile)
        self.get_column_header_for_number(['proteincol'], pepheader)