'taxonomy_id',
'host_organism',
'host_taxonomy_id',
'organelle',
'organism_classification',
#'references',
'comments',
'cross_references',
'keywords',
'seqinfo',
'features',
'sequence',
]
with open(datafile, "r", encoding="ascii") as data:
my_records = list(parse_txt(data))
with open(datafile, "r", encoding="ascii") as data:
biopython_records = list(SwissProt.parse(data))
#####################################################################
# END - Test stuff for parse_txt
#####################################################################
#####################################################################
# Test stuff for parse_txt_atomic
#####################################################################
EXPECTED_ANNOTATIONS = [
"P62140: FUNCTION-Dephosphorylates the 'Ser-418' residue of FOXP3 in regulatory T- cells (Treg) from patients with rheumatoid arthritis, thereby inactivating FOXP3 and rendering Treg cells functionally defective - ECO:0000269-PubMed:23396208",
'P62140: FUNCTION-Protein phosphatase that associates with over 200 regulatory proteins to form highly specific holoenzymes which dephosphorylate hundreds of biological targets - ECO:0000269-None',
'P62140: FUNCTION-Protein phosphatase (PP1) is essential for cell division, it participates in the regulation of glycogen metabolism, muscle contractility and protein synthesis - ECO:0000269-None',
def test_parser_with_unsupported_parameter_int():
with pytest.raises(NotImplementedError):
for record in up.parse_txt(1):
pass
def test_parser_with_unsupported_parameter_dict():
d = {1: 'some'}
with pytest.raises(NotImplementedError):
for record in up.parse_txt(d):
pass
def test_parser_with_Path_instance():
p = pathlib.Path(TEST_DATA_LOCATION)
for record in up.parse_txt(p):
assert record.primary_accession == EXPECTED_ACC
def test_parser_with_str_path():
for record in up.parse_txt(TEST_DATA_LOCATION):
assert record.primary_accession == EXPECTED_ACC
def test_parser_with_WSResponse():
mock = WSResponse(None)
with open(TEST_DATA_LOCATION, 'r') as infile:
mock.text = infile.read()
for record in up.parse_txt(mock):
assert record.primary_accession == EXPECTED_ACC
def test_parser_with_StringIO():
with open(TEST_DATA_LOCATION, 'r') as infile:
content = infile.read()
stringio = StringIO(content)
for record in up.parse_txt(stringio):
assert record.primary_accession == EXPECTED_ACC
def test_parser_with_file_object():
with open(TEST_DATA_LOCATION, 'r') as infile:
for record in up.parse_txt(infile):
assert record.primary_accession == EXPECTED_ACC
def test_ignore_lowercase_entries():
datafile = os.path.join(base_dir, 'SwissProt', 'contains_lowercase.txl')
with open(datafile, 'r') as infile:
entries = list(up.parse_txt(infile))
assert len(entries) == 23
"""
import pytest
import os
from Bio import SwissProt
import prunito.uniprot as up
# Import paths for data files
base_dir = os.path.dirname(__file__)
filename = 'one_sp_entry.txl'
#filename = 'many_sp_entries.txl'
#datafile = os.path.join('SwissProt', filename)
datafile = os.path.join(base_dir, 'SwissProt', filename)
with open(datafile, "r", encoding="ascii") as data:
my_record = list(up.parse_txt(data))
with open(datafile, "r", encoding="ascii") as data:
biopython_record = SwissProt.read(data)
def test_wrong_format_paramater_for_search():
with pytest.raises(ValueError):
up.search('test', frmt='xsd')
def test_uppercase_format_parameter_works_for_search():
pass
def test_object_is_record_instance():