def test_process_ptms():
ptm_file = join(test_dir, 'POST_TRANSLATIONAL_MODIFICATIONS.txt')
seq_file = join(test_dir, 'PROTEIN_SEQUENCES.txt')
hp = hprd.process_flat_files(id_file, ptm_file=ptm_file, seq_file=seq_file)
assert isinstance(hp, hprd.HprdProcessor)
assert isinstance(hp.statements, list)
assert len(hp.statements) == 13
s0 = hp.statements[0]
assert isinstance(s0, Phosphorylation)
assert s0.enz.name == 'MAPK1'
assert s0.enz.db_refs == {
'UP': 'P28482',
'HGNC': '6871',
'EGID': '5594',
'REFSEQ_PROT': 'NP_002736.3'
}
assert s0.sub.name == 'TCF3'
assert s0.sub.db_refs == {
'UP': 'P15923',
'HGNC': '11633',
'EGID': '6929',
'REFSEQ_PROT': 'NP_003191.1'
}
assert s0.residue == 'T'
assert s0.position == '355'
assert len(s0.evidence) == 1
assert s0.evidence[0].pmid == '14592976'
assert s0.evidence[0].source_api == 'hprd'
assert s0.evidence[0].annotations['evidence'] == ['in vivo']
assert s0.evidence[0].annotations['site_motif'] == \
{'motif': 'NFSSSPSTPVGSPQG', 'respos': 8,
'off_by_one': False}
def test_process_complexes():
cplx_file = join(test_dir, 'PROTEIN_COMPLEXES.txt')
hp = hprd.process_flat_files(id_file, complexes_file=cplx_file)
assert isinstance(hp, hprd.HprdProcessor)
assert isinstance(hp.statements, list)
assert len(hp.statements) == 3
s0 = hp.statements[0]
assert isinstance(s0, Complex)
assert len(s0.members) == 3
assert set([ag.name for ag in s0.members]) == \
set(['ASCL1', 'TCF3', 'MEF2C'])
assert s0.members[0].db_refs == \
{'HGNC': '738', 'UP': 'P50553', 'EGID': '429',
'REFSEQ_PROT': 'NP_004307.2'}
assert s0.members[1].db_refs == \
{'HGNC': '11633', 'UP': 'P15923', 'EGID': '6929',
'REFSEQ_PROT': 'NP_003191.1'}
assert s0.members[2].db_refs == \
{'HGNC': '6996', 'UP': 'Q06413', 'EGID': '4208',
'REFSEQ_PROT': 'NP_002388.2'}
assert len(s0.evidence) == 2
assert s0.evidence[0].pmid == '8900141'
assert s0.evidence[0].source_api == 'hprd'
assert s0.evidence[0].annotations['evidence'] == ['in vivo']
assert s0.evidence[0].source_id == ('http://hprd.org/interactions?'
'hprd_id=00011&isoform_id=00011_1'
'&isoform_name=Isoform_1')
assert s0.evidence[1].pmid == '8948587'
def _get_statements(self):
import tarfile
import requests
from indra.sources import hprd
# Download the files.
hprd_base = 'http://www.hprd.org/RELEASE9/'
resp = requests.get(hprd_base + 'HPRD_FLAT_FILES_041310.tar.gz')
tmp_dir = tempfile.mkdtemp('hprd_files')
tmp_tarfile = os.path.join(tmp_dir, 'hprd_files.tar.gz')
with open(tmp_tarfile, 'wb') as f:
f.write(resp.content)
# Extract the files.
with tarfile.open(tmp_tarfile, 'r:gz') as tf:
tf.extractall(tmp_dir)
# Find the relevant files.
dirs = os.listdir(tmp_dir)
for files_dir in dirs:
if files_dir.startswith('FLAT_FILES'):
break
files_path = os.path.join(tmp_dir, files_dir)
file_names = {
'id_mappings_file': 'HPRD_ID_MAPPINGS',
'complexes_file': 'PROTEIN_COMPLEXES',
'ptm_file': 'POST_TRANSLATIONAL_MODIFICATIONS',
'ppi_file': 'BINARY_PROTEIN_PROTEIN_INTERACTIONS',
'seq_file': 'PROTEIN_SEQUENCES'
}
kwargs = {
kw: os.path.join(files_path, fname + '.txt')
for kw, fname in file_names.items()
}
# Run the processor
hp = hprd.process_flat_files(**kwargs)
# Filter out exact duplicates
unique_stmts, dups = \
extract_duplicates(_expanded(hp.statements),
key_func=KeyFunc.mk_and_one_ev_src)
print('\n'.join(str(dup) for dup in dups))
return unique_stmts
def test_process_ppis():
ppi_file = join(test_dir, 'BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt')
hp = hprd.process_flat_files(id_file, ppi_file=ppi_file)
assert isinstance(hp, hprd.HprdProcessor)
assert isinstance(hp.statements, list)
assert len(hp.statements) == 5
s0 = hp.statements[0]
assert isinstance(s0, Complex)
assert len(s0.members) == 2
assert set([ag.name for ag in s0.members]) == set(['ITGA7', 'CHRNA1'])
assert s0.members[0].db_refs == \
{'HGNC': '6143', 'UP': 'Q13683', 'EGID': '3679',
'REFSEQ_PROT': 'NP_001138468.1'}
assert s0.members[1].db_refs == \
{'HGNC': '1955', 'UP': 'P02708', 'EGID': '1134',
'REFSEQ_PROT': 'NP_001034612.1'}
assert len(s0.evidence) == 1
assert s0.evidence[0].pmid == '10910772'
assert s0.evidence[0].source_api == 'hprd'
assert s0.evidence[0].annotations['evidence'] == ['in vivo']
assert s0.evidence[0].source_id == ('http://hprd.org/interactions?'
'hprd_id=02761&isoform_id=02761_1'
'&isoform_name=Isoform_1')
def test_process_ptms_no_seq():
ptm_file = join(test_dir, 'POST_TRANSLATIONAL_MODIFICATIONS.txt')
hp = hprd.process_flat_files(id_file, ptm_file=ptm_file)