def test_add_domains_file():
test_data_dir = shephard.get_data('test_data')
fasta_file = '%s/%s' % (test_data_dir, 'testset_1.fasta')
domain_file = '%s/%s' % (test_data_dir, 'TS1_domains_idr.tsv')
P = uniprot.uniprot_fasta_to_proteome(fasta_file)
interfaces.si_domains.add_domains_from_file(P, domain_file)
# this should fail because already added
with pytest.raises(ProteinException):
interfaces.si_domains.add_domains_from_file(P, domain_file)
P = uniprot.uniprot_fasta_to_proteome(fasta_file)
interfaces.si_domains.add_domains_from_file(P, domain_file, autoname=True)
print('')
P = uniprot.uniprot_fasta_to_proteome(fasta_file)
interfaces.si_domains.add_domains_from_file(P, domain_file, autoname=False)
# autoname allows 2 apparetly identical domain files to be added
interfaces.si_domains.add_domains_from_file(P, domain_file, autoname=True)
# autoname allows 2 apparetly identical domain files to be added
P = uniprot.uniprot_fasta_to_proteome(fasta_file)
interfaces.si_domains.add_domains_from_file(P,
domain_file,
autoname=False,
skip_bad=True)
def test_si_site_add_from_file_test_robustness():
TS1 = uniprot.uniprot_fasta_to_proteome('%s/%s' %
(test_data_dir, 'testset_1.fasta'))
# this should fail - skip_bad influences skipping
with pytest.raises(ProteinException) as e_info:
si_sites.add_sites_from_file(
TS1,
'%s/%s' % (test_data_dir, 'ts1_bonus_sites_bad.tsv'),
skip_bad=True)
with pytest.raises(ProteinException) as e_info:
si_sites.add_sites_from_file(
TS1,
'%s/%s' % (test_data_dir, 'ts1_bonus_sites_bad.tsv'),
skip_bad=False)
# but if we load in with safe=False will skip over the bad site
si_sites.add_sites_from_file(TS1,
'%s/%s' %
(test_data_dir, 'ts1_bonus_sites_bad.tsv'),
safe=False)
O00470 = TS1.protein('O00470')
assert len(O00470) == 390
def test_add_domain_attribute():
test_data_dir = shephard.get_data('test_data')
fasta_file = '%s/%s' % (test_data_dir, 'testset_1.fasta')
domain_file = '%s/%s' % (test_data_dir, 'TS1_domains_idr.tsv')
P = uniprot.uniprot_fasta_to_proteome(fasta_file)
interfaces.si_domains.add_domains_from_file(P, domain_file)
prot = P.protein('O00401')
domain = prot.domains[0]
domain.add_attribute('test_attribute', 1)
assert domain.attribute('test_attribute') == 1
# this should fail
with pytest.raises(DomainException):
domain.add_attribute('test_attribute', 20)
# because the operation above should have failed, this too should
# have failed
assert domain.attribute('test_attribute') == 1
domain.add_attribute('test_attribute', 20, safe=False)
assert domain.attribute('test_attribute') == 20
assert len(domain.attributes) == 1
domain.add_attribute('another_test_attribute', 'testval')
assert len(domain.attributes) == 2
with pytest.raises(DomainException):
assert domain.attribute('does not exist') == 20
# check this returns none
assert domain.attribute('does not exist', safe=False) is None
def test_write_domain_with_attributes():
# this setup was also tested in test_add_domain_attribute
test_data_dir = shephard.get_data('test_data')
fasta_file = '%s/%s' % (test_data_dir, 'testset_1.fasta')
domain_file = '%s/%s' % (test_data_dir, 'TS1_domains_idr.tsv')
P = uniprot.uniprot_fasta_to_proteome(fasta_file)
interfaces.si_domains.add_domains_from_file(P, domain_file)
prot = P.protein('O00401')
domain = prot.domains[0]
domain.add_attribute('test_attribute_1', 1)
domain.add_attribute('test_attribute_cat', 'cat')
def test_getter_properies():
TS1 = uniprot.uniprot_fasta_to_proteome('%s/%s' %
(test_data_dir, 'testset_1.fasta'))
prot = TS1.protein('O00470')
assert len(TS1.protein('O00470')) == 390
assert prot.name == "sp|O00470|MEIS1_HUMAN Homeobox protein Meis1 OS=H**o sapiens OX=9606 GN=MEIS1 PE=1 SV=1"
assert str(
prot.proteome) == "[Proteome]: Sequence dataset with 9 protein records"
assert prot.unique_ID == 'O00470'
assert prot.get_residue(1) == 'M'
assert prot.get_residue(2) == 'A'
assert prot.get_residue(390) == 'M'
with pytest.raises(ProteinException):
assert prot.get_residue(0) == 'M'
#assert protein.get_sequence = '
assert prot.sequence == 'MAQRYDDLPHYGGMDGVGIPSTMYGDPHAARSMQPVHHLNHGPPLHSHQYPHTAHTNAMAPSMGSSVNDALKRDKDAIYGHPLFPLLALIFEKCELATCTPREPGVAGGDVCSSESFNEDIAVFAKQIRAEKPLFSSNPELDNLMIQAIQVLRFHLLELEKVHELCDNFCHRYISCLKGKMPIDLVIDDREGGSKSDSEDITRSANLTDQPSWNRDHDDTASTRSGGTPGPSSGGHTSHSGDNSSEQGDGLDNSVASPSTGDDDDPDKDKKRHKKRGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRAVSQGTPYNPDGQPMGGFVMDGQQHMGIRAPGPMSGMGMNMGMEGQWHYM'
assert prot.get_sequence_region(1, 5) == 'MAQRY'
assert prot.get_sequence_region(390, 390) == 'M'
with pytest.raises(ProteinException):
assert prot.get_sequence_region(390, 391) == 'M'
assert prot.get_sequence_region(380, 390) == 'NMGMEGQWHYM'
assert prot.get_sequence_context(1, 10) == 'MAQRYDDLPHY'
assert prot.get_sequence_context(10, 3) == 'DLPHYGG'
assert prot.get_sequence_context(390, 5) == 'GQWHYM'
assert prot.get_sequence_context(
50, 450
) == 'MAQRYDDLPHYGGMDGVGIPSTMYGDPHAARSMQPVHHLNHGPPLHSHQYPHTAHTNAMAPSMGSSVNDALKRDKDAIYGHPLFPLLALIFEKCELATCTPREPGVAGGDVCSSESFNEDIAVFAKQIRAEKPLFSSNPELDNLMIQAIQVLRFHLLELEKVHELCDNFCHRYISCLKGKMPIDLVIDDREGGSKSDSEDITRSANLTDQPSWNRDHDDTASTRSGGTPGPSSGGHTSHSGDNSSEQGDGLDNSVASPSTGDDDDPDKDKKRHKKRGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRAVSQGTPYNPDGQPMGGFVMDGQQHMGIRAPGPMSGMGMNMGMEGQWHYM'
with pytest.raises(ProteinException):
prot.get_sequence_context(400, 3)
assert prot.check_sequence_is_valid() is True
assert len(prot.attributes) == 0
assert prot.attribute('TEST', safe=False) is None
assert len(prot.tracks) == 0
assert len(prot.track_names) == 0
assert prot.track('TEST', safe=False) is None
def test_si_site_add_file_read_robustness():
TS1 = uniprot.uniprot_fasta_to_proteome('%s/%s' %
(test_data_dir, 'testset_1.fasta'))
# thsi should fail - malformatted line
with pytest.raises(InterfaceException) as e_info:
si_sites.add_sites_from_file(
TS1,
'%s/%s' % (test_data_dir, 'ts1_bonus_sites_bad2.tsv'),
skip_bad=False)
si_sites.add_sites_from_file(TS1,
'%s/%s' %
(test_data_dir, 'ts1_bonus_sites_bad2.tsv'),
skip_bad=True)
assert len(TS1.sites) == 4
def test_si_site_add_from_file():
TS1 = uniprot.uniprot_fasta_to_proteome('%s/%s' %
(test_data_dir, 'testset_1.fasta'))
si_sites.add_sites_from_file(
TS1, '%s/%s' % (test_data_dir, 'ts1_bonus_sites.tsv'))
O00470 = TS1.protein('O00470')
# check length
assert len(O00470) == 390
assert len(O00470.site(1)) == 1
assert len(O00470.site(390)) == 1
# get site a position 2 that doesn't exist
with pytest.raises(ProteinException) as e_info:
O00470.site(2)
# get site at position 2 that doesn't exsit
assert O00470.site(2, safe=False) == None
def build_proteome(fn):
return uniprot.uniprot_fasta_to_proteome('%s/%s' % (test_data_dir, fn))
def test_add_protein():
# creating proteome and adding protein
test_data_dir = shephard.get_data('test_data')
P = uniprot.uniprot_fasta_to_proteome('%s/%s' %
(test_data_dir, 'testset_1.fasta'))
assert len(P.protein('O00401')) == 505
assert len(P.protein('O00470')) == 390
assert len(P.protein('O00472')) == 640
assert len(P.protein('O00499')) == 593
assert len(P.protein('O00629')) == 521
assert len(P.protein('O00712')) == 420
assert len(P.protein('O00716')) == 465
assert len(P.protein('O14786')) == 923
assert len(P.protein('Q9UJX3')) == 599
# creating a proteome from a FASTA file (using defaul unique key)
P = fasta.fasta_to_proteome('%s/%s' % (test_data_dir, 'testset_1.fasta'))
assert len(P.protein('1')) == 390
assert len(P.protein('2')) == 640
assert len(P.protein('3')) == 593
assert len(P.protein('4')) == 521
assert len(P.protein('5')) == 420
assert len(P.protein('6')) == 465
assert len(P.protein('7')) == 923
assert len(P.protein('8')) == 599
# create a proteome where FASTA header is used as uniqueID
P = fasta.fasta_to_proteome('%s/%s' % (test_data_dir, 'testset_1.fasta'),
use_header_as_unique_ID=True)
assert len(
P.protein(
'sp|O00470|MEIS1_HUMAN Homeobox protein Meis1 OS=H**o sapiens OX=9606 GN=MEIS1 PE=1 SV=1'
)) == 390
assert len(
P.protein(
'sp|O00472|ELL2_HUMAN RNA polymerase II elongation factor ELL2 OS=H**o sapiens OX=9606 GN=ELL2 PE=1 SV=2'
)) == 640
assert len(
P.protein(
'sp|O00499|BIN1_HUMAN Myc box-dependent-interacting protein 1 OS=H**o sapiens OX=9606 GN=BIN1 PE=1 SV=1'
)) == 593
assert len(
P.protein(
'sp|O00629|IMA3_HUMAN Importin subunit alpha-3 OS=H**o sapiens OX=9606 GN=KPNA4 PE=1 SV=1'
)) == 521
assert len(
P.protein(
'sp|O00712|NFIB_HUMAN Nuclear factor 1 B-type OS=H**o sapiens OX=9606 GN=NFIB PE=1 SV=2'
)) == 420
assert len(
P.protein(
'sp|O00716|E2F3_HUMAN Transcription factor E2F3 OS=H**o sapiens OX=9606 GN=E2F3 PE=1 SV=1'
)) == 465
assert len(
P.protein(
'sp|O14786|NRP1_HUMAN Neuropilin-1 OS=H**o sapiens OX=9606 GN=NRP1 PE=1 SV=3'
)) == 923
assert len(
P.protein(
'sp|Q9UJX3|APC7_HUMAN Anaphase-promoting complex subunit 7 OS=H**o sapiens OX=9606 GN=ANAPC7 PE=1 SV=4'
)) == 599
# check manually adding proteomes
local_seq = 'PPPPP'
P.add_protein(local_seq, '5pp', 'U5P')
assert P.protein('U5P').sequence == local_seq
assert P.protein('U5P').name == '5pp'
# should trigger exception
with pytest.raises(ProteomeException):
P.add_protein(local_seq, '5pp', 'U5P')
P.add_protein('ASDF', '5pp', 'U5P', force_overwrite=True)
assert P.protein('U5P').sequence == 'ASDF'
protein_list = []
p1 = {
'sequence': 'ASDFGH',
'name': "Test protein 1",
'unique_ID': 1.23,
"attributes": None
}
protein_list.append(p1)
# check this works
P = proteome.Proteome(protein_list)
print(P.proteins)
assert P.protein(1.23).sequence == 'ASDFGH'
assert P.protein("1.23").sequence == 'ASDFGH'
P.remove_protein(1.23)
with pytest.raises(ProteomeException):
assert P.protein(1.23).sequence == 'ASDFGH'
def test_add_site():
# build new proteome
TS1 = uniprot.uniprot_fasta_to_proteome('%s/%s' %
(test_data_dir, 'testset_1.fasta'))