class GOBlastRunTestCase(unittest.TestCase): def setUp(self): self.my_blast_db = None self.my_blast_file = None self.my_blast_outfile = "./test/data/hddb_test.blast.xml" self.my_blast_exe = None self.e_value_threshold = 1e-130 self.length_threshold = .85 self.processors = None self.multi_hits = True self.ba = GOBlastFilter(self.my_blast_exe, self.my_blast_db, self.my_blast_file, self.e_value_threshold, self.length_threshold, blast_processors=self.processors, multi_hits = self.multi_hits) self.outfile_handle = open(self.my_blast_outfile) self.records = self.ba.runBlast(self.outfile_handle) self.filtered = self.ba.filterBlast(self.records) def testHitID(self): assert 124598 == self.filtered[str(3)][0].hit_id, 'wrong hit_id' def testQueryID(self): assert 3 == self.filtered[str(3)][0].query_id, 'wrong query_id'
def setUp(self): self.my_blast_db = None self.my_blast_file = None self.my_blast_outfile = "./test/data/hddb_test.blast.xml" self.my_blast_exe = None self.e_value_threshold = 1e-130 self.length_threshold = .85 self.processors = None self.multi_hits = True self.ba = GOBlastFilter(self.my_blast_exe, self.my_blast_db, self.my_blast_file, self.e_value_threshold, self.length_threshold, blast_processors=self.processors, multi_hits = self.multi_hits) self.outfile_handle = open(self.my_blast_outfile) self.records = self.ba.runBlast(self.outfile_handle) self.filtered = self.ba.filterBlast(self.records)
def goIEA(self): self.ba = GOBlastFilter(self.my_blast_exe, self.my_blast_db, self.my_blast_file, self.e_value_threshold, self.length_threshold, blast_processors=self.processors, multi_hits=self.multi_hits) if self.blast_checkpoint: self.records = self.ba.runBlast() #kdrew: a little kludgey, if not running blast but are going to filter from blast file, read in the blast out file elif self.filter_checkpoint: outfile_handle = open(self.my_blast_outfile) self.records = self.ba.runBlast(result_handle=outfile_handle) for blast_record in self.records: filtered_record = self.ba.filterBlastOne(blast_record) if None != filtered_record: if self.multi_hits: seqs = list() for f_rec in filtered_record: seqs.append(f_rec.hit_id) terms = self.mg.getGoTerms(seqs, full=True, ancestors=False) self.store_terms(filtered_record[0].query_id, terms, seqs) else: print filtered_record.hit_id terms = self.mg.getGoTerms(filtered_record.hit_id, full=True, ancestors=False) self.store_terms(filtered_record.query_id, terms, [filtered_record.hit_id])
class GO_IEA():
def __init__(self, config_file=None, section=None):
config = ConfigParser.RawConfigParser()
config.read(config_file)
if None == config_file:
self._default_init()
return
#kdrew: blast parameters
self.my_blast_db = config.get(section, 'blast_db')
self.my_blast_file = config.get(section, 'blast_file')
self.my_blast_outfile = config.get(section, 'blast_outfile')
self.my_blast_exe = config.get(section, 'blast_exe')
self.e_value_threshold = config.getfloat(section, 'blast_e_value_threshold')
self.length_threshold = config.getfloat(section, 'blast_length_threshold')
self.processors = config.getint(section, 'blast_processors')
self.multi_hits = config.getboolean(section, 'multi_hits')
self.blast_checkpoint = config.getboolean(section,'blast_checkpoint')
self.filter_checkpoint = config.getboolean(section,'filter_checkpoint')
#kdrew: database parameters
self.sql_user= config.get(section, 'sql_user')
self.sql_password= config.get(section, 'sql_password')
self.mygo_host= config.get(section, 'mygo_host')
self.mygo_db = config.get(section, 'mygo_db')
self.store_host= config.get(section, 'store_host')
self.store_db = config.get(section, 'store_db')
#kdrew: store table parameters
self.store_table = config.get(section, 'store_table_name')
self.store_evidence_code = config.get(section, 'store_evidence_code')
self.store_source = config.get(section, 'store_source')
#kdrew: mygo parameters
self.evidence_codes_str = config.get(section,'evidence_codes')
self.evidence_codes = list(self.evidence_codes_str.split(','))
self.conn = MySQLdb.connect(host=self.store_host, user=self.sql_user, passwd=self.sql_password, db=self.store_db)
self.mg = Mygo(self.sql_user,self.sql_password, self.mygo_host, e_codes = self.evidence_codes, db_name=self.mygo_db)
self.mg.connect()
def goIEA(self):
self.ba = GOBlastFilter(self.my_blast_exe, self.my_blast_db, self.my_blast_file, self.e_value_threshold, self.length_threshold, blast_processors=self.processors, multi_hits=self.multi_hits)
if self.blast_checkpoint:
self.records = self.ba.runBlast()
#kdrew: a little kludgey, if not running blast but are going to filter from blast file, read in the blast out file
elif self.filter_checkpoint:
outfile_handle = open(self.my_blast_outfile)
self.records = self.ba.runBlast(result_handle=outfile_handle)
for blast_record in self.records:
filtered_record = self.ba.filterBlastOne(blast_record)
if None != filtered_record:
if self.multi_hits:
seqs = list()
for f_rec in filtered_record:
seqs.append(f_rec.hit_id)
terms = self.mg.getGoTerms(seqs, full=True, ancestors=False)
self.store_terms(filtered_record[0].query_id, terms, seqs)
else:
print filtered_record.hit_id
terms = self.mg.getGoTerms(filtered_record.hit_id, full=True, ancestors=False)
self.store_terms(filtered_record.query_id, terms, [filtered_record.hit_id])
def store_terms(self, query_id, terms, hit_seqs):
cursor = self.conn.cursor(MySQLdb.cursors.DictCursor)
create_query = """CREATE TABLE IF NOT EXISTS """+self.store_table+""" (
id int(11) NOT NULL auto_increment,
sequence_key int(11) NOT NULL default '0',
domain_sequence_key int(11) NOT NULL,
acc varchar(20) NOT NULL default '',
name varchar(255) NOT NULL,
term_type enum('molecular_function','biological_process','cellular_component') NOT NULL,
evidence_code varchar(50) NOT NULL default '',
xref_dbname varchar(50) NOT NULL,
xref_key varchar(50) NOT NULL,
probability double NOT NULL,
llr double NOT NULL,
level int(11) NOT NULL,
source varchar(50) NOT NULL default 'unknown',
hit_seqs mediumtext NOT NULL default '',
insert_date date default NULL,
timestamp timestamp NOT NULL default CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP,
PRIMARY KEY (id),
UNIQUE KEY sequence_key (sequence_key,domain_sequence_key,acc,evidence_code,source),
KEY evidence_code (evidence_code)
)"""
cursor.execute(create_query)
query = "INSERT INTO "+self.store_table+" (sequence_key, acc, name, term_type, evidence_code, source,hit_seqs, insert_date) VALUES (%s, %s,%s,%s,%s,%s,%s,%s)"
query_list = list()
for term in terms:
query_list.append((query_id, term.acc, term.name, term.type, self.store_evidence_code, self.store_source,",".join(map(str,hit_seqs)), datetime.date.today()))
while query_list:
small_data, query_list = query_list[:EXECUTEMANY_SIZE], query_list[EXECUTEMANY_SIZE:]
cursor.executemany(query,small_data)