def test__write_idmap_csv(self):
# arrange
fastafile_name = '1_A'
accession_num = 'Q99985'
length = 751
sbjct_end = 565
sbjct_start = 28
full_name = 'Semaphorin-3C'
altname = 'Semaphorin-E'
flags = 'Precursor'
expected_csv = 'sequence_id,accession_num,length,full_name,altname,flags,start_pos,end_pos\n' + \
fastafile_name + ',' + accession_num + ',' + str(length) + ',' + full_name + ',' + \
altname + ',' + flags + ',' + str(sbjct_start) + ',' + str(sbjct_end) + '\n'
expected_path_output_blastp_csvfile = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, fastafile_name + '_idmaps',
'idmap_swsprt.csv')
idmap = {
'sequence_id': fastafile_name,
'accession_num': accession_num,
'length': 751,
'full_name': full_name,
'altname': altname,
'flags': flags,
'start_pos': 28,
'end_pos': 565
}
# act
IdProt._write_idmap_csv(path_output=TPLS.MC_TESTS_OUTPUT.value,
idmap=idmap)
# assert
with open(expected_path_output_blastp_csvfile) as csv_opened:
csv = csv_opened.read()
self.assertTrue(expected_csv, csv)
def start_blast(path_input_fastafiles: list,
path_output: str,
write_idmaps_for_mysldb=True,
write_csv=True,
write_xml=True,
write_json=False,
use_multithread=False):
"""
:param path_input_fastafiles:
:param path_output:
:param write_idmaps_for_mysldb:
:param write_csv:
:param write_xml:
:param write_json:
:param use_multithread:
:return:
"""
if use_multithread:
print('')
# Scheduler._launch_thread(target=IdProt.map_seq_to_swsprt_acc_id_and_write_files,
# args=[path_input_fastas_dir, path_output, write_idmaps_for_mysldb, write_csv,
# write_xml, write_json])
# Scheduler._launch_process_threadpool(target=IdProt., args=)
else:
IdProt.map_seq_to_swsprt_acc_id_and_write_files(
path_input_fastafiles=path_input_fastafiles,
path_output=path_output,
write_idmaps_for_mysqldb=write_idmaps_for_mysldb,
write_csv=write_csv,
write_xml=write_xml,
write_json=write_json)
def test_map_seq_to_swsprt_acc_id_and_write_files(self):
# act
IdProt.map_seq_to_swsprt_acc_id_and_write_files(
path_input_fastafiles=self.PATH_TESTS_INPUT_FASTA_1_A,
path_output=TPLS.MC_TESTS_OUTPUT.value,
write_idmaps_for_mysqldb=False,
write_csv=False,
write_xml=False,
write_json=False)
def test__extract_names_flags_(self):
# arrange
hit_def = 'RecName: Full=Mastermind-like protein 1; Short=Mam-1'
expected_result = {self.RECNAME_SRCH_STR: 'Mastermind-like protein 1'}
# act
actual_result = IdProt._extract_names_flags(hit_def,
self.RECNAME_SRCH_STR,
self.ALTNAME_SRCH_STR,
self.FLAGS_SRCH_STR)
# assert
self.assertDictEqual(expected_result, actual_result)
def test_map_seq_to_swsprt_acc_id_and_write_files_1_A(
self, mock_qblast, mock__write_raw_blast_xml):
# arrange
len_1_A = len(self.FASTA_SEQ_1_A)
query_len = align_len = idents = q_end = len_1_A
acc = 'Q99985'
hit_len = 751
hit_start_pos = 28
hit_end_pos = hit_start_pos + query_len - 1
hit_def = 'RecName: Full=Semaphorin-3C; AltName: Full=Semaphorin-E; Short=Sema E; Flags: Precursor'
expected_align_list_1_A = [{
'accession_num': acc,
'length': hit_len,
'hit_def': hit_def,
'hsp_dict': {
'align_length': align_len,
'gaps': self.ZERO_GAP,
'identities': idents,
'query_end': q_end,
'query_start': self.QSTRT_1,
'sbjct_end': hit_end_pos,
'sbjct_start': hit_start_pos
}
}]
expected_qblast_dict_list_1_A = [{
'database':
self.SWSPRT_DB,
'database_seqs_num':
self.SWSPRT_PROTS_NUM,
'query_length':
query_len,
'query_seq_id':
self.NAME_1_A,
'identical_aligns_list':
expected_align_list_1_A
}]
with open(self.PATH_TESTS_REFFILES_BLASTP_1_A_XML) as test_1_A_xml:
mock_qblast.return_value = test_1_A_xml
mock__write_raw_blast_xml.return_value = self.PATH_TESTS_REFFILES_BLASTP_1_A_XML
path_output_blastp_1_A = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, self.DIR_1_A)
# act
result_dict_list = IdProt.map_seq_to_swsprt_acc_id_and_write_files(
path_input_fastafiles=self.PATH_TESTS_INPUT_FASTA_1_A,
path_output=path_output_blastp_1_A,
write_idmaps_for_mysqldb=False,
write_csv=False,
write_xml=False,
write_json=False)
# assert
self.maxDiff = None
self.assertListEqual(expected_qblast_dict_list_1_A, result_dict_list)
self.assertDictEqual(expected_qblast_dict_list_1_A[0],
result_dict_list[0])
def test__write_dict_to_json_file(self):
# arrange
fastafile_name = "1_A"
accession_num = "Q99985"
length = 751
sbjct_end = 565
sbjct_start = 28
full_name = "Semaphorin-3C"
altname = "Semaphorin-E"
flags = "Precursor"
idmap = {
"sequence_id": fastafile_name,
"accession_num": accession_num,
"length": length,
"full_name": full_name,
"altname": altname,
"flags": flags,
"start_pos": sbjct_start,
"end_pos": sbjct_end
}
expected_path_output_blastp_jsonfile = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, fastafile_name + "_idmaps",
"idmap_swsprt.json")
path_ref_files_blastp_1_A_jsonfile = os.path.join(
TPLS.MC_TESTS_REFFILES.value, TPLS.DIR_BLASTP.value,
fastafile_name + '_idmaps', 'idmap_swsprt.json')
expected_json = str(idmap)
# act
IdProt._write_idmap_jsonfile(path_output=TPLS.MC_TESTS_OUTPUT.value,
idmap=idmap)
# assert
with open(expected_path_output_blastp_jsonfile) as json_opened, \
open(path_ref_files_blastp_1_A_jsonfile) as ref_json_opened:
json = json_opened.read()
expected_json = ref_json_opened.read()
self.assertEqual(expected_json, json)
def test__extract_names_flags_24_C(self):
# arrange
hit_def = 'RecName: Full=Catenin delta-1; AltName: Full=Cadherin-associated Src substrate; Short=CAS; ' \
'AltName: Full=p120 catenin; Short=p120(ctn); AltName: Full=p120(cas)'
expected_result = {
self.RECNAME_SRCH_STR: 'Catenin delta-1',
self.ALTNAME_SRCH_STR: 'Cadherin-associated Src substrate'
}
# act
actual_result = IdProt._extract_names_flags(hit_def,
self.RECNAME_SRCH_STR,
self.ALTNAME_SRCH_STR,
self.FLAGS_SRCH_STR)
# assert
self.assertDictEqual(expected_result, actual_result)
def test__extract_names_flags_1_A(self):
# arrange
hit_def = 'RecName: Full=Semaphorin-3C; AltName: Full=Semaphorin-E; Short=Sema E; Flags: Precursor'
expected_result = {
self.RECNAME_SRCH_STR: 'Semaphorin-3C',
self.ALTNAME_SRCH_STR: 'Semaphorin-E',
self.FLAGS_SRCH_STR: 'Precursor'
}
# act
actual_result = IdProt._extract_names_flags(hit_def,
self.RECNAME_SRCH_STR,
self.ALTNAME_SRCH_STR,
self.FLAGS_SRCH_STR)
# assert
self.assertDictEqual(expected_result, actual_result)
def test__write_idmap_xml(self):
# arrange
fastafile_name = '1_A'
accession_num = 'Q99985'
length = 751
sbjct_end = 565
sbjct_start = 28
full_name = 'Semaphorin-3C'
altname = 'Semaphorin-E'
flags = 'Precursor'
expected_xml = '<?xml version="1.0" encoding="UTF-8"?>\n<sequence_id="1_A">\n<accession_num>\n' + \
accession_num + '</accession_num>\n<length>' + str(length) + '</length>\n<full name>' + \
full_name + '</full name>\n<altname>' + altname + '</altname>\n<flags>' + flags + \
'</flags>\n<start pos>' + str(sbjct_start) + '</start pos>\n<end pos>' + str(sbjct_end) + \
'</end pos>\n</sequence_id\n'
expected_path_output_blastp_xmlfile = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, fastafile_name + '_idmaps',
'idmap_swsprt.xml')
idmap = {
'sequence_id': fastafile_name,
'accession_num': accession_num,
'length': 751,
'full_name': full_name,
'altname': altname,
'flags': flags,
'start_pos': 28,
'end_pos': 565
}
# act
IdProt._write_idmap_xml(path_output=TPLS.MC_TESTS_OUTPUT.value,
idmap=idmap)
# assert
with open(expected_path_output_blastp_xmlfile) as xml_opened:
xml = xml_opened.read()
self.assertTrue(expected_xml, xml)
def test__extract_names_flags_11_B(self):
# arrange
hit_def = 'RecName: Full=B-cell lymphoma 6 protein; Short=BCL-6; AltName: Full=B-cell lymphoma 5 protein; ' \
'Short=BCL-5; AltName: Full=Protein LAZ-3; AltName: Full=Zinc finger and BTB domain-containing ' \
'protein 27; AltName: Full=Zinc finger protein 51'
expected_result = {
self.RECNAME_SRCH_STR: 'B-cell lymphoma 6 protein',
self.ALTNAME_SRCH_STR: 'B-cell lymphoma 5 protein'
}
# act
actual_result = IdProt._extract_names_flags(hit_def,
self.RECNAME_SRCH_STR,
self.ALTNAME_SRCH_STR,
self.FLAGS_SRCH_STR)
# assert
self.assertDictEqual(expected_result, actual_result)
def test__extract_names_flags_18_B(self):
# arrange
hit_def = 'RecName: Full=Alkaline phosphatase, tissue-nonspecific isozyme; Short=AP-TNAP; ' \
'Short=TNSALP; AltName: Full=Alkaline phosphatase liver/bone/kidney isozyme; Flags: Precursor'
expected_result = {
self.RECNAME_SRCH_STR:
'Alkaline phosphatase, tissue-nonspecific isozyme',
self.ALTNAME_SRCH_STR:
'Alkaline phosphatase liver/bone/kidney isozyme',
self.FLAGS_SRCH_STR: 'Precursor'
}
# act
actual_result = IdProt._extract_names_flags(hit_def,
self.RECNAME_SRCH_STR,
self.ALTNAME_SRCH_STR,
self.FLAGS_SRCH_STR)
# assert
self.assertDictEqual(expected_result, actual_result)
def test__extract_names_flags_37_B(self):
# arrange
hit_def = 'RecName: Full=Neurogenic locus notch homolog protein 1; Short=Notch 1; Short=hN1; AltName: ' \
'Full=Translocation-associated notch protein TAN-1; Contains: RecName: Full=Notch 1 extracellular ' \
'truncation; Short=NEXT; Contains: RecName: Full=Notch 1 intracellular domain; Short=NICD; ' \
'Flags: Precursor'
expected_result = {
self.RECNAME_SRCH_STR: 'Neurogenic locus notch homolog protein 1',
self.ALTNAME_SRCH_STR:
'Translocation-associated notch protein TAN-1',
self.FLAGS_SRCH_STR: 'Precursor'
}
# act
actual_result = IdProt._extract_names_flags(hit_def,
self.RECNAME_SRCH_STR,
self.ALTNAME_SRCH_STR,
self.FLAGS_SRCH_STR)
# assert
self.assertDictEqual(expected_result, actual_result)
def test__write_raw_blast_xml(self):
# arrange
GUM.linux_remove_all_files_in_dir(
os.path.join(TPLS.MC_TESTS_OUTPUT_BLASTP.value,
self.DIR_1_A + self.UNDR_SCR_ID_MAPS))
path_ref_blast_output_file = os.path.join(TPLS.MC_TESTS_REFFILES.value,
TPLS.DIR_BLASTP.value,
self.XML_FILE_1_A)
with open(path_ref_blast_output_file) as ref_xml_1_A_open:
id_map_fasta_dir = self.DIR_1_A + self.UNDR_SCR_ID_MAPS
expected_path_output_blastp_xmlfile = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, id_map_fasta_dir,
self.XML_FILE_1_A)
# act
path_output_blastp_xmlfile = IdProt._write_raw_blast_xml(
path_output=TPLS.MC_TESTS_OUTPUT.value,
fastafilename=self.DIR_1_A,
blastp_result=ref_xml_1_A_open)
# assert
self.assertTrue(os.path.exists(expected_path_output_blastp_xmlfile))
self.assertEqual(expected_path_output_blastp_xmlfile,
path_output_blastp_xmlfile)
path_output_blastp = sys.argv[4]
write_idmaps_for_mysldb = sys.argv[5] == 'True'
write_csv = sys.argv[6] == 'True'
write_xml = sys.argv[7] == 'True'
write_json = sys.argv[8] == 'True'
for path_fastafile in path_input_fastafile_list:
with open(path_fastafile) as fastafile_opened:
fastafile_name = path_fastafile.split('/')[-1].split('.')[0]
jobname = 'BLSTP_' + fastafile_name
Cluster.write_job_q_bash(jobname=jobname, path_job_q_dir=path_config_job, queue='all.q', memory_limit_GB='3',
cluster_node='hodor1.vib')
path_output_blastp_fastaname = GUM.os_makedirs(path_output_blastp, fastafile_name)
os.chdir(path_output_blastp_fastaname)
Cluster.run_job_q(path_job_q_dir=path_config_job)
Cluster.wait_for_grid_engine_job_to_complete(grid_engine_job_prefix_or_full_name=jobname)
path_raw_blstp_xml = IdProt._write_raw_blast_xml(path_output, fastafile_name,
blastp_result=NCBIWWW.qblast(
program=Biopy.BlastParam.BLST_P.value,
database=Biopy.BlastParam.SWSPRT.value,
sequence=fastafile_opened.read(),
entrez_query=Biopy.BlastParam.HOMSAP_ORG.value,
alignments=Biopy.BlastParam.MAX_ALIGN_20.value,
hitlist_size=Biopy.BlastParam.MAX_HIT_20.value))
blastp_dict = Biopy.parse_filter_blastp_xml_to_dict(path_raw_blstp_xml, fastafile_name, path_fastafile)
# blastp_dict_list.append(blastp_dict)
if write_idmaps_for_mysldb:
IdProt._write_idmaps_for_mysqldb(path_output, blastp_dict, write_csv=write_csv, write_xml=write_xml,
write_json=write_json)
def test__write_idmaps_for_mysqldb(self):
# arrange
GUM.linux_remove_all_files_in_dir(
os.path.join(TPLS.MC_TESTS_OUTPUT_BLASTP.value,
self.DIR_1_A + self.UNDR_SCR_ID_MAPS))
fastafile_name = self.DIR_1_A
query_length = 538
database_used = 'swissprot'
database_seqs_num = 20379
accession_num = 'Q99985'
length = 751
sbjct_end = 565
sbjct_start = 28
identical_aligns_list = [{
'accession_num':
accession_num,
'length':
length,
'hit_def':
'RecName: Full=Semaphorin-3C; AltName: Full=Semaphorin-E; Short=Sema E; '
'Flags: Precursor',
'hsp_dict': {
'align_length': 538,
'gaps': 0,
'identities': 538,
'query_end': 538,
'query_start': 1,
'sbjct_end': sbjct_end,
'sbjct_start': sbjct_start
}
}]
blastp_dict = {
'query_seq_id': fastafile_name,
'query_length': query_length,
'database': database_used,
'database_seqs_num': database_seqs_num,
'identical_aligns_list': identical_aligns_list
}
full_name = 'Semaphorin-3C'
altname = 'Semaphorin-E'
flags = 'Precursor'
expected_csv = 'sequence_id,accession_num,length,full_name,altname,flags,start_pos,end_pos\n' + \
fastafile_name + ',' + accession_num + ',' + str(length) + ',' + full_name + ',' + \
altname + ',' + flags + ',' + str(sbjct_start) + ',' + str(sbjct_end) + '\n'
expected_xml = '<?xml version="1.0" encoding="UTF-8"?>\n<sequence_id id="1_A">\n\t<accession_num>' + \
accession_num + '</accession_num>\n\t<length>' + str(length) + '</length>\n\t<full_name>' + \
full_name + '</full_name>\n\t<altname>' + altname + '</altname>\n\t<flags>' + flags + \
'</flags>\n\t<start_pos>' + str(sbjct_start) + '</start_pos>\n\t<end_pos>' + str(sbjct_end) + \
'</end_pos>\n</sequence_id>\n'
expected_json = {
"sequence_id": fastafile_name,
"accession_num": accession_num,
"length": 751,
"full_name": full_name,
"altname": altname,
"flags": flags,
"start_pos": 28,
"end_pos": 565
}
expected_path_output_blastp_xmlfile = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, self.DIR_1_A + '_idmaps',
'idmap_swsprt.xml')
expected_path_output_blastp_csvfile = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, self.DIR_1_A + '_idmaps',
'idmap_swsprt.csv')
expected_path_output_blastp_jsonfile = os.path.join(
TPLS.MC_TESTS_OUTPUT_BLASTP.value, self.DIR_1_A + '_idmaps',
'idmap_swsprt.json')
# act
IdProt._write_idmaps_for_mysqldb(
path_output=TPLS.MC_TESTS_OUTPUT.value,
blastp_dict=blastp_dict,
write_xml=True,
write_csv=True,
write_json=True)
# assert
with open(expected_path_output_blastp_csvfile) as csv_opened:
csv = csv_opened.read()
self.assertEqual(expected_csv, csv)
with open(expected_path_output_blastp_xmlfile) as xml_opened:
xml = xml_opened.read()
self.assertEqual(expected_xml, xml)
path_ref_files_blastp_1_A_jsonfile = os.path.join(
TPLS.MC_TESTS_REFFILES.value, TPLS.DIR_BLASTP.value,
fastafile_name + '_idmaps', 'idmap_swsprt.json')
with open(expected_path_output_blastp_jsonfile) as json_opened, \
open(path_ref_files_blastp_1_A_jsonfile) as ref_json_opened:
json = json_opened.read()
expected_json = ref_json_opened.read()
self.assertEqual(expected_json, json)