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Viewing changes to Tests/test_SeqUtils.py

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2014-06-08 10:25:35 UTC
  • mfrom: (1.1.22)
  • Revision ID: package-import@ubuntu.com-20140608102535-ebgnhcpcrum3i3w8
Tags: 1.64+dfsg-1
http://bugs.debian.org/750845
* New upstream version
* Build-Depends raxml only on those architectures where it is available
  Closes: #750845

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Tests/test_SeqUtils.py
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from Bio.Alphabet import single_letter_alphabet
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from Bio.Seq import Seq, MutableSeq
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from Bio.SeqRecord import SeqRecord
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from Bio.SeqUtils import GC, quick_FASTA_reader, seq1, seq3
 
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from Bio.SeqUtils import GC, seq1, seq3
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from Bio.SeqUtils.lcc import lcc_simp, lcc_mult
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from Bio.SeqUtils.CheckSum import crc32, crc64, gcg, seguid
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from Bio.SeqUtils.CodonUsage import CodonAdaptationIndex
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                        + "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
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                        + "YCCSYAGSSTWVFGGGTKLTVL"
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    def test_quick_fasta_reader(self):
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        dna_fasta_filename = "Fasta/f002"
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        tuple_records = quick_FASTA_reader(dna_fasta_filename)
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        self.assertEqual(len(tuple_records), 3)
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        seq_records = list(SeqIO.parse(dna_fasta_filename, "fasta"))
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        self.assertEqual(len(seq_records), 3)
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        for tuple_record, seq_record in zip(tuple_records, seq_records):
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            self.assertEqual(tuple_record, (seq_record.description, str(seq_record.seq)))
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    def test_codon_usage_ecoli(self):
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        """Test Codon Adaptation Index (CAI) using default E. coli data."""
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        CAI = CodonAdaptationIndex()