e888f185c3877e7c34aa6fa7d65e684fe872e867,anvio/contigops.py,GenbankToAnvio,sanity_check,#GenbankToAnvio#,243

Before Change

        filesnpaths.is_file_exists(self.input_genbank_path)

        try:
            SeqIO.parse(open(self.input_genbank_path, "r"), "genbank")
        except Exception as e:
            raise ConfigError("Someone didn"t like your unput "genbank" file :/ Here"s what they said\
                               about it: "%s"." % e)

After Change

    def sanity_check(self):
        if self.output_file_prefix and (self.output_fasta_path or self.output_functions_path or self.output_gene_calls_path):
            raise ConfigError("Your arguments contain an output file prefix, and other output file paths. You can either\
                               define a prefix, and the output files would be named accordingly (such as "PREFIX-extenral-gene-calls",\
                               "PREFIX-external-functions.txt", and "PREFIX-contigs.fa"), ORRR you can set output file names\
                               or paths for each of these files independently. You can also leave it as is for default file names to\
                               be used. But you can"t mix everything together and confuse us here.")

        self.output_fasta_path = self.output_fasta_path or "contigs.fa"
        self.output_functions_path = self.output_functions_path or "external-functions.txt"
        self.output_gene_calls_path = self.output_gene_calls_path or "external-gene-calls.txt"

        if self.output_file_prefix:
            J = lambda x: "-".join([self.output_file_prefix, x])
            self.output_fasta_path = J(self.output_fasta_path)
            self.output_functions_path = J(self.output_functions_path)
            self.output_gene_calls_path = J(self.output_gene_calls_path)

        filesnpaths.is_output_file_writable(self.output_fasta_path)
        filesnpaths.is_output_file_writable(self.output_functions_path)
        filesnpaths.is_output_file_writable(self.output_gene_calls_path)
        filesnpaths.is_file_exists(self.input_genbank_path)

        files_already_exist = [f for f in [self.output_fasta_path, self.output_functions_path, self.output_gene_calls_path] if os.path.exists(f)]
        if len(files_already_exist):
            raise ConfigError("Some of the output files already exist :/ Anvi"o feels uneasy about simply overwriting\
                               them and would like to outsource that risk to you. Please either use different output\
                               file names, or delete these files and come back: "%s"" % (", ".join(files_already_exist)))


    def process(self):
        self.sanity_check()

        output_fasta = {}

Instances