def test_change_template():
test_lib = olg.peptide_library('AAAA')
fname = os.path.join(os.path.dirname(__file__), 'test_file.inp')
test_lib.load_designs(fname)
test_lib.change_template('CCC')
assert test_lib.template.seq == 'CCC'
def test_lib_default_creation():
"""Create default library"""
test_lib = olg.peptide_library('AAAA')
assert test_lib.lib_name == 'AAAA'
assert test_lib.codon_usage_species == 'human'
assert test_lib.include_template
assert len(test_lib) == 1
assert test_lib._aalibrary['AAAA'] == 'AAAA_OO_0'
def test_restrict_double_bias_var_generation():
# test_lib generation of all variant with restriction variants
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
test_lib.generate_single_variants(bias=['G', 'C'], bias_type='restrict')
assert len(test_lib) == 3
def test_bias_var_generation():
# test_lib generation of all variant with exclusion variant
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
test_lib.generate_single_variants(bias=['A'])
assert len(test_lib) == 54
def test_random_trim():
# Test random removing
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
test_lib.generate_single_variants(bias=['A', 'G'])
test_lib.random_purge(21)
assert len(test_lib) == 30
def test_lib_creation_from_a_file():
# test_lib to load designs and add restriction enzymes
test_lib = olg.peptide_library('AAA',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
fname = os.path.join(os.path.dirname(__file__), 'test_file.inp')
test_lib.load_designs(fname)
assert len(test_lib) == 2
assert test_lib._aalibrary['AAC']
assert test_lib._aalibrary['AAI']
def test_simple_var_generation():
# test_lib generation of all simple variants
# by default option
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
test_lib.generate_single_variants()
test_lib.write(file_name='wtestvar.fasta')
assert len(test_lib) == 57
assert os.path.isfile('wtestvar.fasta')
os.remove('wtestvar.fasta')
def test_add_restriction_enzymes():
test_lib = olg.peptide_library('AAA',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
fname = os.path.join(os.path.dirname(__file__), 'test_file.inp')
test_lib.load_designs(fname)
# add restriction enzymes as a list, nop name
test_lib.add_restriction_enzyme(['GCTGCC', 'GCAGCT'])
# add restriction enzyme has a dict, with id
test_lib.add_restriction_enzyme({'free': 'GCAGCG'})
assert len(test_lib.restriction_enzymes) == 3
def test_load_json():
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
# test_lib json generation permutations
fname = os.path.join(os.path.dirname(__file__),
'test_permutations_cfg.json')
test_lib.permutations_json(fname)
assert len(test_lib._aalibrary) == 6
test_lib.write()
assert os.path.isfile('test-lib.fasta')
os.remove('test-lib.fasta')
def test_lib_custom_creation():
# create a new library abd check if user set values works
test_lib = olg.peptide_library('AAA',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
assert test_lib.lib_name != 'AAA'
assert test_lib.codon_usage_species != 'human'
assert test_lib.include_template == False
assert test_lib.CONSTANT_F == 'AGT'
assert test_lib.CONSTANT_R == 'XXX'
assert len(test_lib) == 0
def test_random_generation():
# test_lib random generation
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
test_lib.generate_random_variants(how_many=10, mutant_kind=[2])
test_lib.write(add_stop_end=False)
olg.check_lib_integrty(
'test-lib.fasta',
'CCC',
15,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
restriction_site=test_lib.restriction_enzymes.values())
# test_lib random generation in range
test_lib._aalibrary = dict()
test_lib.generate_random_variants(how_many=10,
mutant_kind=[2],
inrange=[2, 3])
# test_lib write without extend and stop codons
# test_lib inframe
# All sequence are the same at the beging
test_lib.write(add_stop_end=False)
assert os.path.isfile('test-lib.fasta')
os.remove('test-lib.fasta')
test_lib._aalibrary = dict()
test_lib.generate_inframe_variants(frame_size=2)
test_lib.write(add_stop_end=False)
olg.check_lib_integrty(
'test-lib.fasta',
'CCC',
15,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
restriction_site=test_lib.restriction_enzymes.values())
os.remove('test-lib.fasta')
def test_double_bias_var_generation():
# test_lib generation of all variant with exclusion variant more than one
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
test_lib.generate_single_variants(bias=['A', 'G'])
assert len(test_lib) == 51
# check if the library is free of Ala and Gly
for seq in test_lib._aalibrary.keys():
assert not 'A' in seq
# raise 'error in bias'
assert not 'G' in seq
def test_writing_options():
# Test writing
test_lib = olg.peptide_library('CCC',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
test_lib.generate_single_variants(bias=['A', 'G'])
# extend sequence to 25
test_lib.write(file_name='test-lib.fasta', extend=25)
olg.check_lib_integrty(
'test-lib.fasta',
'CCC',
25,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
restriction_site=test_lib.restriction_enzymes.values())
os.remove('test-lib.fasta')
def test_write_library():
# create a lib from a file
test_lib = olg.peptide_library('AAA',
include_template=False,
CONSTANT_F='AGT',
CONSTANT_R='XXX',
lib_name='test-lib',
codon_usage_species='E.coli')
fname = os.path.join(os.path.dirname(__file__), 'test_file.inp')
test_lib.load_designs(fname)
# add restriction enzymes
test_lib.add_restriction_enzyme(['GCTGCC', 'GCAGCT'])
test_lib.add_restriction_enzyme({'free': 'GCAGCG'})
# test_lib write functions
test_lib.write(file_name='wtest0.fasta')
# test different restriction enzymes
test_lib.add_restriction_enzyme(['GCCGCG', 'GCTGCT'])
test_lib.write(file_name='wtest1.fasta')
test_lib.add_restriction_enzyme(['GCTGCG'])
test_lib.write(file_name='wtest2.fasta')
test_lib.add_restriction_enzyme(['GCTGCA'])
test_lib.write(file_name='wtest3.fasta')
test_lib.add_restriction_enzyme(['GCGGCG'])
test_lib.write(file_name='wtest4.fasta')
# assert files
for i in range(5):
assert os.path.isfile('wtest{}.fasta'.format(i))
# rmove test files
for i in range(5):
os.remove('wtest{}.fasta'.format(i))
