def __init__(self, config_file=None, section=None):
config = ConfigParser.RawConfigParser()
config.read(config_file)
if None == config_file:
self._default_init()
return
#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_previous_db = config.get(section, 'mygo_previous_db')
self.mygo_recent_db = config.get(section, 'mygo_recent_db')
#kdrew: store table parameters
self.store_host = config.get(section, 'store_host')
self.store_db = config.get(section, 'store_db')
self.store_table_name = config.get(section, 'store_table_name')
self.store_source = config.get(section, 'store_source')
self.store_evidence_code = config.get(section, 'store_evidence_code')
self.annotation_host= config.get(section, 'annotation_host')
self.annotation_db = config.get(section, 'annotation_db')
self.annotation_table_recent = config.get(section, 'annotation_table_name_recent')
self.annotation_table_previous = config.get(section, 'annotation_table_name_previous')
self.previous_source = config.get(section, 'previous_source')
self.recent_source = config.get(section, 'recent_source')
#kdrew: mygo parameters
self.recent_evidence_codes_str = config.get(section,'recent_evidence_codes')
self.recent_evidence_codes = list(self.recent_evidence_codes_str.split(','))
self.previous_evidence_codes_str = config.get(section,'previous_evidence_codes')
self.previous_evidence_codes = list(self.previous_evidence_codes_str.split(','))
self.term_types_str = config.get(section,'term_types')
self.term_types = list(self.term_types_str.split(','))
self.conn = MySQLdb.connect(host=self.annotation_host, user=self.sql_user, passwd=self.sql_password, db=self.annotation_db)
self.store_conn = MySQLdb.connect(host=self.store_host, user=self.sql_user, passwd=self.sql_password, db=self.store_db)
self.justStore = GO_IEA_Just_Store(self.store_conn, self.store_table_name, self.store_evidence_code, self.store_source)
self.mg = Mygo(self.sql_user,self.sql_password, self.mygo_host, e_codes = self.recent_evidence_codes, db_name=self.mygo_recent_db)
self.mg.connect()
class DiffAnnotations():
def __init__(self, config_file=None, section=None):
config = ConfigParser.RawConfigParser()
config.read(config_file)
if None == config_file:
self._default_init()
return
#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_previous_db = config.get(section, 'mygo_previous_db')
self.mygo_recent_db = config.get(section, 'mygo_recent_db')
#kdrew: store table parameters
self.store_host = config.get(section, 'store_host')
self.store_db = config.get(section, 'store_db')
self.store_table_name = config.get(section, 'store_table_name')
self.store_source = config.get(section, 'store_source')
self.store_evidence_code = config.get(section, 'store_evidence_code')
self.annotation_host= config.get(section, 'annotation_host')
self.annotation_db = config.get(section, 'annotation_db')
self.annotation_table_recent = config.get(section, 'annotation_table_name_recent')
self.annotation_table_previous = config.get(section, 'annotation_table_name_previous')
self.previous_source = config.get(section, 'previous_source')
self.recent_source = config.get(section, 'recent_source')
#kdrew: mygo parameters
self.recent_evidence_codes_str = config.get(section,'recent_evidence_codes')
self.recent_evidence_codes = list(self.recent_evidence_codes_str.split(','))
self.previous_evidence_codes_str = config.get(section,'previous_evidence_codes')
self.previous_evidence_codes = list(self.previous_evidence_codes_str.split(','))
self.term_types_str = config.get(section,'term_types')
self.term_types = list(self.term_types_str.split(','))
self.conn = MySQLdb.connect(host=self.annotation_host, user=self.sql_user, passwd=self.sql_password, db=self.annotation_db)
self.store_conn = MySQLdb.connect(host=self.store_host, user=self.sql_user, passwd=self.sql_password, db=self.store_db)
self.justStore = GO_IEA_Just_Store(self.store_conn, self.store_table_name, self.store_evidence_code, self.store_source)
self.mg = Mygo(self.sql_user,self.sql_password, self.mygo_host, e_codes = self.recent_evidence_codes, db_name=self.mygo_recent_db)
self.mg.connect()
#kdrew: find difference beween terms using set theory
def diff_terms(self, recent_terms, previous_terms):
recent_set = set(recent_terms)
previous_set = set(previous_terms)
return list(recent_set - previous_set)
def diff(self):
cursor = self.conn.cursor(MySQLdb.cursors.DictCursor)
#kdrew: get annotations from recent
#kdrew: get annotations from previous
#kdrew: compare
previous_codes_fmt = "'"+"','".join(self.previous_evidence_codes)+"'"
print self.previous_evidence_codes
print previous_codes_fmt
recent_codes_fmt = "'"+"','".join(self.recent_evidence_codes)+"'"
print self.recent_evidence_codes
print recent_codes_fmt
type_fmt = "'"+"','".join(self.term_types)+"'"
print self.term_types
print type_fmt
#kdrew: get all sequence keys with a specific term_type (ie. molecular_function) and a given evidence code
query_seqs = """select distinct hig.sequence_key from """+self.annotation_table_recent+""" as hig where hig.term_type in (%s) and hig.evidence_code in (%s)""" % (type_fmt, recent_codes_fmt)
print query_seqs
cursor.execute(query_seqs)
seqs = cursor.fetchall()
print len(seqs)
#kdrew: for every sequence key
for seq in seqs:
sequence_key = seq["sequence_key"]
#kdrew: get all annotations for the sequence key from the earlier database
query = """select distinct t2.acc, t2.name, t2.term_type
from """+self.annotation_table_previous+""" as hig, """+self.mygo_previous_db+""".term as t, """+self.mygo_previous_db+""".term as t2, """+self.mygo_previous_db+""".graph_path as gp
where gp.term2_id = t.id and t.acc = hig.acc and t2.id = gp.term1_id and hig.term_type in (%s) and t2.term_type in (%s) and hig.evidence_code in (%s) and hig.sequence_key = %s""" % (type_fmt,type_fmt,previous_codes_fmt,str(sequence_key))
cursor.execute(query)
previous_term_rows = cursor.fetchall()
previous_terms = rows2terms(previous_term_rows, self.previous_evidence_codes,full=True)
#kdrew: get all annotations for the sequence key from the recent database
query2 = """select distinct t2.acc, t2.name, t2.term_type
from """+self.annotation_table_recent+""" as hig, """+self.mygo_recent_db+""".term as t, """+self.mygo_recent_db+""".term as t2, """+self.mygo_recent_db+""".graph_path as gp
where gp.term2_id = t.id and t.acc = hig.acc and t2.id = gp.term1_id and hig.term_type in (%s) and t2.term_type in (%s) and hig.evidence_code in (%s) and hig.sequence_key = %s""" % (type_fmt,type_fmt,recent_codes_fmt,str(sequence_key))
cursor.execute(query2)
recent_term_rows = cursor.fetchall()
recent_terms = rows2terms(recent_term_rows, self.recent_evidence_codes,full=True)
new_terms = self.diff_terms(recent_terms, previous_terms)
print "sequence_key: ", sequence_key, " new terms: ", new_terms
self.justStore.store_terms(sequence_key, new_terms)
