INNER CODE UNIT · Python

is_input_fasta_file_valid

nickjcroucher/gubbins · python/gubbins/ValidateFastaAlignment.py:18

    def is_input_fasta_file_valid(self):
      try:
          if not self.does_each_sequence_have_the_same_length():
              print("Each sequence must be the same length")
              return False
          if not self.are_sequence_names_unique():
              print("All sequence names in the fasta file must be unique")
              return False
          if not self.does_each_sequence_have_a_name_and_genomic_data():
              print("Each sequence must have a name and some genomic data")
              return False
      except:
          return False
      return True

    def does_each_sequence_have_a_name_and_genomic_data(self):
      with open(self.input_filename, "r") as input_handle:
        alignments = AlignIO.parse(input_handle, "fasta")

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