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src/b/i/biopython-1.63/Tests/test_CodonUsage.py   biopython(Download)
# now generate an index from a file
if os.path.exists("./CodonUsage/HighlyExpressedGenes.txt"):
    X.generate_index("./CodonUsage/HighlyExpressedGenes.txt")
elif os.path.exists("./Tests/CodonUsage/HighlyExpressedGenes.txt"):
    X.generate_index("./Tests/CodonUsage/HighlyExpressedGenes.txt")

src/b/i/biopython-HEAD/Tests/test_CodonUsage.py   biopython(Download)
# now generate an index from a file
if os.path.exists("./CodonUsage/HighlyExpressedGenes.txt"):
    X.generate_index("./CodonUsage/HighlyExpressedGenes.txt")
elif os.path.exists("./Tests/CodonUsage/HighlyExpressedGenes.txt"):
    X.generate_index("./Tests/CodonUsage/HighlyExpressedGenes.txt")

src/b/i/biopython-HEAD/Tests/test_SeqUtils.py   biopython(Download)
        # Note - this needs a FASTA file which containing non-ambiguous DNA coding
        # sequences - which should each be a whole number of codons.
        CAI.generate_index(dna_fasta_filename)
        # Now check codon usage index (CAI) using this species
        self.assertEqual(record.annotations["source"],

src/b/i/biopython-1.63/Tests/test_SeqUtils.py   biopython(Download)
        # Note - this needs a FASTA file which containing non-ambiguous DNA coding
        # sequences - which should each be a whole number of codons.
        CAI.generate_index(dna_fasta_filename)
        # Now check codon usage index (CAI) using this species
        self.assertEqual(record.annotations["source"],