def test_return_list():
test_data_dir = protfasta._get_data('test_data')
duplicate_filename = '%s/testset_duplicate_seqs.fasta' % (test_data_dir)
duplicate_record = '%s/testset_duplicate.fasta' % (test_data_dir)
simple_filename = '%s/testset_1.fasta' % (test_data_dir)
x = protfasta.read_fasta(simple_filename, duplicate_sequence_action='fail')
assert type(x) == dict
x = protfasta.read_fasta(simple_filename,
duplicate_sequence_action='fail',
return_list=True)
assert type(x) == list
# show we can use return_list to read in a FASTA file with two identical records (note when we did this before and
# return_list=False then len(x) == 2 because the dictionary overwrites
x = protfasta.read_fasta(duplicate_record,
duplicate_record_action='ignore',
return_list=True,
expect_unique_header=False)
assert len(x) == 3
x = protfasta.read_fasta(duplicate_record,
duplicate_record_action='remove',
return_list=True,
expect_unique_header=False)
assert len(x) == 2
def test_duplicate_sequence_action():
test_data_dir = protfasta._get_data('test_data')
duplicate_filename = '%s/testset_duplicate_seqs.fasta' % (test_data_dir)
simple_filename = '%s/testset_1.fasta' % (test_data_dir)
# this should be fine because simple_filename is valid
assert len(
protfasta.read_fasta(simple_filename,
duplicate_sequence_action='fail')) == 9
# this should be fine because simple_filename is valid
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(duplicate_filename,
duplicate_sequence_action='fail')
# this should be fine because simple_filename is valid
assert len(
protfasta.read_fasta(duplicate_filename,
duplicate_sequence_action='ignore')) == 3
# remove duplciate sequence
assert len(
protfasta.read_fasta(duplicate_filename,
duplicate_sequence_action='remove',
verbose=True)) == 2
# note only the sequences are duplicate, not the record
assert len(
protfasta.read_fasta(duplicate_filename,
duplicate_record_action='remove',
verbose=True)) == 3
def test_read_fasta_standard():
test_data_dir = protfasta._get_data('test_data')
simple_filename = '%s/testset_1.fasta' % (test_data_dir)
x = protfasta.read_fasta(simple_filename)
assert len(x) == 9
# check can read in a sequence correctly
assert x[test_data['test1'][0]] == test_data['test1'][1]
def test_alignment_files():
test_data_dir = protfasta._get_data('test_data')
f1 = '%s/aligned_seq_all_valid.fasta' % (test_data_dir)
f2 = '%s/aligned_seq_all_valid_convertable.fasta' % (test_data_dir)
f3 = '%s/aligned_seq_all_valid_unconvertable.fasta' % (test_data_dir)
x = protfasta.read_fasta(f1, alignment=True)
assert x['Seq1'] == 'A-----CDEFGHIKLMNPQRSTVWY'
# this should fail because by default dashes are invalid and fail upon invalid is set to true
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(f1)
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(f1, alignment=1)
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(f2, alignment=True)
x = protfasta.read_fasta(f2,
alignment=True,
invalid_sequence_action='convert')
assert x['Seq1'] == 'A-----CDEFGHIKLMNPQRSTVWY'
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(f3,
alignment=True,
invalid_sequence_action='convert')
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(f3, alignment=True)
x = protfasta.read_fasta(f3,
alignment=True,
invalid_sequence_action='convert-ignore')
assert x['Seq2'] == 'ACDEFGHIKL-----MNPQRSTVWYN'
x = protfasta.read_fasta(f3,
alignment=True,
invalid_sequence_action='remove')
assert len(x) == 0
x = protfasta.read_fasta(f1,
alignment=True,
invalid_sequence_action='remove')
assert len(x) == 3
x = protfasta.read_fasta(f1, invalid_sequence_action='remove')
assert len(x) == 0
def test_duplicate_record_action():
test_data_dir = protfasta._get_data('test_data')
duplicate_filename = '%s/testset_duplicate.fasta' % (test_data_dir)
simple_filename = '%s/testset_1.fasta' % (test_data_dir)
# this should be fine because simple_filename is valid
assert len(
protfasta.read_fasta(simple_filename,
duplicate_record_action='fail')) == 9
# this should fail because duplicate_filename has duplicates
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(duplicate_filename,
duplicate_record_action='fail')
# this should fail because this combination of options (i.e. implicit expect_unique=True)
# will throw and error
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(duplicate_filename,
duplicate_record_action='ignore')
# THIS should fail because even though we've said remove, we are still expecting uniqe
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(duplicate_filename,
duplicate_record_action='remove')
x = protfasta.read_fasta(duplicate_filename,
duplicate_record_action='remove',
expect_unique_header=False)
assert len(x) == 2
x = protfasta.read_fasta(duplicate_filename,
duplicate_record_action='ignore',
expect_unique_header=False,
return_list=True)
assert len(x) == 3
# this is not goood, BUT if we say expect uniuqe false, ignore duplicates and dont return a list we will use the first entry
x = protfasta.read_fasta(duplicate_filename,
duplicate_record_action='ignore',
expect_unique_header=False)
assert len(x) == 2
# if we ignore or remove, same difference
x = protfasta.read_fasta(duplicate_filename,
duplicate_record_action='remove',
expect_unique_header=False)
assert len(x) == 2
def test_header_parser():
test_data_dir = protfasta._get_data('test_data')
simple_filename = '%s/testset_1.fasta' % (test_data_dir)
def d(s):
return s[0:10]
def d_dumb(s):
return "asas"
def d_bad():
return "asas"
def d_bad2(s):
return 1
x = protfasta.read_fasta(simple_filename, header_parser=d)
assert len(x) == 9
assert x[test_data['test1'][0][0:10]] == test_data['test1'][1]
# this dumb combination of settings means we overwrite the headers
a = protfasta.read_fasta(simple_filename,
header_parser=d_dumb,
duplicate_sequence_action='ignore',
expect_unique_header=False)
assert len(a) == 1
# now we at least avoid overwriting by setting the return type to be a list
a = protfasta.read_fasta(simple_filename,
header_parser=d_dumb,
duplicate_sequence_action='ignore',
expect_unique_header=False,
return_list=True)
assert len(a) == 9
# should fail because headers are duplicate
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(simple_filename, header_parser=d_dumb)
# bool only
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(simple_filename, header_parser=d_bad)
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(simple_filename, header_parser=d_bad2)
def test_expect_unique_header_toggle():
test_data_dir = protfasta._get_data('test_data')
simple_filename = '%s/testset_1.fasta' % (test_data_dir)
x = protfasta.read_fasta(simple_filename, expect_unique_header=False)
assert len(x) == 9
assert x[test_data['test1'][0]] == test_data['test1'][1]
x = protfasta.read_fasta(simple_filename, expect_unique_header=True)
assert len(x) == 9
assert x[test_data['test1'][0]] == test_data['test1'][1]
# bool only
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(simple_filename,
expect_unique_header='dog')
# bool only
with pytest.raises(ProtfastaException):
assert protfasta.read_fasta(simple_filename, expect_unique_header=1)
def test_sequences_with_bad_chars():
test_data_dir = protfasta._get_data('test_data')
badchar_filename = '%s/test_data_with_bad_chars.fa' % (test_data_dir)
nonstandard_filename = '%s/test_data_with_nonstandard_chars.fa' % (
test_data_dir)
# expect this to fail because invalid characters are in here...
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(badchar_filename)
# expect this to fail because non-standard characters are in here...
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(nonstandard_filename)
# expect this to fail because invalid characters are in here (explicitlty pass 'fail')
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(badchar_filename,
invalid_sequence_action='fail')
# expect this to fail because non-standard characters are in here... (explicitlty pass 'fail')
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(nonstandard_filename,
invalid_sequence_action='fail')
# make sure we can ignore bad chars regardless of if they're convertable or not
assert len(
protfasta.read_fasta(nonstandard_filename,
invalid_sequence_action='ignore')) == 4
assert len(
protfasta.read_fasta(badchar_filename,
invalid_sequence_action='ignore')) == 4
# make sure we can convert nonstandard names
assert len(
protfasta.read_fasta(nonstandard_filename,
invalid_sequence_action='convert')) == 4
# make sure we can't convert invalid character names
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(badchar_filename,
invalid_sequence_action='convert')
# make sure we can convert and ignore (even when ignore is not needed)
assert len(
protfasta.read_fasta(nonstandard_filename,
invalid_sequence_action='convert-ignore')) == 4
# make sure we can convert and ignore (even when ignore is needed)
assert len(
protfasta.read_fasta(badchar_filename,
invalid_sequence_action='convert-ignore')) == 4
# make sure we can remove sequences with bad chars regardless of if they're convertable or not
assert len(
protfasta.read_fasta(nonstandard_filename,
invalid_sequence_action='remove')) == 0
assert len(
protfasta.read_fasta(badchar_filename,
invalid_sequence_action='remove')) == 0
#CD = {'-': '', '.': 'A', 'X':'Y'}
CD = {'.': 'A'}
# this should fail because no conversion has been requested
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(nonstandard_filename,
correction_dictionary=CD)
# THIS should fail because we've overwritten the default dictionary
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(nonstandard_filename,
correction_dictionary=CD,
invalid_sequence_action='convert')
# this should fail because CD does not explain all chars that must be corrected
with pytest.raises(ProtfastaException):
x = protfasta.read_fasta(badchar_filename,
correction_dictionary=CD,
invalid_sequence_action='convert')
CD = {'.': 'A', '-': 'C'}
x = protfasta.read_fasta(badchar_filename,
correction_dictionary=CD,
invalid_sequence_action='convert')
CD = {'.': 'A'}
x = protfasta.read_fasta(badchar_filename,
correction_dictionary=CD,
invalid_sequence_action='convert-ignore')