Python list_ambiguous_codons 예제들

예제 #1

파일: test_CodonTable.py 프로젝트: iriziotis/biopython_bugfixes

 def test_list_ambiguous_codons(self):
     """Check if stop codons are properly extended."""
     self.assertEqual(
         list_ambiguous_codons(["TGA", "TAA"],
                               IUPACData.ambiguous_dna_values),
         ["TGA", "TAA", "TRA"],
     )
     self.assertEqual(
         list_ambiguous_codons(["TAG", "TGA"],
                               IUPACData.ambiguous_dna_values),
         ["TAG", "TGA"],
     )
     self.assertEqual(
         list_ambiguous_codons(["TAG", "TAA"],
                               IUPACData.ambiguous_dna_values),
         ["TAG", "TAA", "TAR"],
     )
     self.assertEqual(
         list_ambiguous_codons(["UAG", "UAA"],
                               IUPACData.ambiguous_rna_values),
         ["UAG", "UAA", "UAR"],
     )
     self.assertEqual(
         list_ambiguous_codons(["TGA", "TAA", "TAG"],
                               IUPACData.ambiguous_dna_values),
         ["TGA", "TAA", "TAG", "TAR", "TRA"],
     )

예제 #2

파일: test_CodonTable.py 프로젝트: MarkusPiotrowski/biopython

 def test_list_ambiguous_codons(self):
     """Check if stop codons are properly extended."""
     self.assertEqual(list_ambiguous_codons(['TGA', 'TAA'],
                                            IUPACData.ambiguous_dna_values),
                      ['TGA', 'TAA', 'TRA'])
     self.assertEqual(list_ambiguous_codons(['TAG', 'TGA'],
                                            IUPACData.ambiguous_dna_values),
                      ['TAG', 'TGA'])
     self.assertEqual(list_ambiguous_codons(['TAG', 'TAA'],
                                            IUPACData.ambiguous_dna_values),
                      ['TAG', 'TAA', 'TAR'])
     self.assertEqual(list_ambiguous_codons(['UAG', 'UAA'],
                                            IUPACData.ambiguous_rna_values),
                      ['UAG', 'UAA', 'UAR'])
     self.assertEqual(list_ambiguous_codons(['TGA', 'TAA', 'TAG'],
                                            IUPACData.ambiguous_dna_values),
                      ['TGA', 'TAA', 'TAG', 'TAR', 'TRA'])

예제 #3

 def test_list_ambiguous_codons(self):
     """Check if stop codons are properly extended."""
     self.assertEqual(list_ambiguous_codons(['TGA', 'TAA'],
                                            IUPACData.ambiguous_dna_values),
                      ['TGA', 'TAA', 'TRA'])
     self.assertEqual(list_ambiguous_codons(['TAG', 'TGA'],
                                            IUPACData.ambiguous_dna_values),
                      ['TAG', 'TGA'])
     self.assertEqual(list_ambiguous_codons(['TAG', 'TAA'],
                                            IUPACData.ambiguous_dna_values),
                      ['TAG', 'TAA', 'TAR'])
     self.assertEqual(list_ambiguous_codons(['UAG', 'UAA'],
                                            IUPACData.ambiguous_rna_values),
                      ['UAG', 'UAA', 'UAR'])
     self.assertEqual(list_ambiguous_codons(['TGA', 'TAA', 'TAG'],
                                            IUPACData.ambiguous_dna_values),
                      ['TGA', 'TAA', 'TAG', 'TAR', 'TRA'])

예제 #4

파일: test_CodonTable.py 프로젝트: addessk/biopython

# Copyright 2008 by Peter C**k.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

from __future__ import print_function

from Bio.Data import IUPACData
from Bio.Data.CodonTable import ambiguous_generic_by_id, ambiguous_generic_by_name
from Bio.Data.CodonTable import ambiguous_rna_by_id, ambiguous_dna_by_id
from Bio.Data.CodonTable import unambiguous_rna_by_id
from Bio.Data.CodonTable import list_ambiguous_codons, TranslationError

#Check the extension of stop codons to include well defined ambiguous ones
assert list_ambiguous_codons(['TGA', 'TAA'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TRA']
assert list_ambiguous_codons(['TAG', 'TGA'],IUPACData.ambiguous_dna_values) == ['TAG', 'TGA']
assert list_ambiguous_codons(['TAG', 'TAA'],IUPACData.ambiguous_dna_values) == ['TAG', 'TAA', 'TAR']
assert list_ambiguous_codons(['UAG', 'UAA'],IUPACData.ambiguous_rna_values) == ['UAG', 'UAA', 'UAR']
assert list_ambiguous_codons(['TGA', 'TAA', 'TAG'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']


#Basic sanity test,
for n in ambiguous_generic_by_id.keys():
    assert ambiguous_rna_by_id[n].forward_table["GUU"] == "V"
    assert ambiguous_rna_by_id[n].forward_table["GUN"] == "V"
    if n != 23 :
        assert ambiguous_rna_by_id[n].forward_table["UUN"] == "X"  # F or L

    assert ambiguous_dna_by_id[n].forward_table["GTT"] == "V"
    if n != 23 :
        assert ambiguous_dna_by_id[n].forward_table["TTN"] == "X"  # F or L

예제 #5

파일: test_CodonTable.py 프로젝트: joshainglis/biopython

# Copyright 2008 by Peter C**k.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

from Bio.Data import IUPACData
from Bio.Data.CodonTable import ambiguous_generic_by_id, ambiguous_generic_by_name
from Bio.Data.CodonTable import ambiguous_rna_by_id, ambiguous_dna_by_id
from Bio.Data.CodonTable import unambiguous_rna_by_id
from Bio.Data.CodonTable import list_ambiguous_codons, TranslationError

#Check the extension of stop codons to include well defined ambiguous ones
assert list_ambiguous_codons(
    ['TGA', 'TAA'], IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TRA']
assert list_ambiguous_codons(['TAG', 'TGA'],
                             IUPACData.ambiguous_dna_values) == ['TAG', 'TGA']
assert list_ambiguous_codons(
    ['TAG', 'TAA'], IUPACData.ambiguous_dna_values) == ['TAG', 'TAA', 'TAR']
assert list_ambiguous_codons(
    ['UAG', 'UAA'], IUPACData.ambiguous_rna_values) == ['UAG', 'UAA', 'UAR']
assert list_ambiguous_codons(
    ['TGA', 'TAA', 'TAG'],
    IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']

#Basic sanity test,
for n in ambiguous_generic_by_id.keys():
    assert ambiguous_rna_by_id[n].forward_table["GUU"] == "V"
    assert ambiguous_rna_by_id[n].forward_table["GUN"] == "V"
    if n != 23:
        assert ambiguous_rna_by_id[n].forward_table["UUN"] == "X"  # F or L

예제 #6

파일: test_CodonTable.py 프로젝트: vincentdavis/biopython

# Copyright 2008 by Peter C**k.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

from __future__ import print_function

from Bio.Data import IUPACData
from Bio.Data.CodonTable import ambiguous_generic_by_id, ambiguous_generic_by_name
from Bio.Data.CodonTable import ambiguous_rna_by_id, ambiguous_dna_by_id
from Bio.Data.CodonTable import unambiguous_rna_by_id
from Bio.Data.CodonTable import list_ambiguous_codons, TranslationError

# Check the extension of stop codons to include well defined ambiguous ones
assert list_ambiguous_codons(["TGA", "TAA"], IUPACData.ambiguous_dna_values) == ["TGA", "TAA", "TRA"]
assert list_ambiguous_codons(["TAG", "TGA"], IUPACData.ambiguous_dna_values) == ["TAG", "TGA"]
assert list_ambiguous_codons(["TAG", "TAA"], IUPACData.ambiguous_dna_values) == ["TAG", "TAA", "TAR"]
assert list_ambiguous_codons(["UAG", "UAA"], IUPACData.ambiguous_rna_values) == ["UAG", "UAA", "UAR"]
assert list_ambiguous_codons(["TGA", "TAA", "TAG"], IUPACData.ambiguous_dna_values) == [
    "TGA",
    "TAA",
    "TAG",
    "TAR",
    "TRA",
]


# Basic sanity test,
for n in ambiguous_generic_by_id:
    assert ambiguous_rna_by_id[n].forward_table["GUU"] == "V"
    assert ambiguous_rna_by_id[n].forward_table["GUN"] == "V"