def run(self): if self.debug: import pdb pdb.set_trace() import MySQLdb mysql_conn = MySQLdb.connect(db=self.dbname, host="banyan.usc.edu", user=self.db_user, passwd=self.db_passwd) mysql_curs = mysql_conn.cursor() from pymodule import get_gene_symbol2gene_id_set gene_symbol2gene_id_set = get_gene_symbol2gene_id_set( mysql_curs, 3702, table="genome.gene_symbol2id", upper_case_gene_symbol=1 ) # 3702 is At's tax id from variation.src.DrawSNPRegion import DrawSNPRegion DrawSNPRegion_ins = DrawSNPRegion( db_user=self.db_user, db_passwd=self.db_passwd, hostname=self.hostname, database=self.dbname, input_fname="/tmp/dumb", output_dir="/tmp", debug=0, ) # input_fname and output_dir are just random stuff gene_annotation = DrawSNPRegion_ins.dealWithGeneAnnotation( self.gene_annotation_picklef, cls_with_db_args=DrawSNPRegion_ins ) self.improveTAIRGeneGFF(self.input_fname, gene_symbol2gene_id_set, gene_annotation, self.output_fname)
def run(self): """ 2008-08-19 """ if self.debug: import pdb pdb.set_trace() db = Stock_250kDB(drivername=self.drivername, username=self.db_user, password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema) db.setup(create_tables=False) import MySQLdb mysql_conn = MySQLdb.connect(db=self.dbname, host='banyan.usc.edu', user=self.db_user, passwd=self.db_passwd) mysql_curs = mysql_conn.cursor() from pymodule import get_gene_symbol2gene_id_set gene_symbol2gene_id_set = get_gene_symbol2gene_id_set( mysql_curs, 3702, table='genome.gene_symbol2id', upper_case_gene_symbol=1) #3702 is At's tax id session = db.session session.begin() self.putGeneListIntoDb(self.input_fname, self.list_type_id, self.list_type_name, gene_symbol2gene_id_set, db, self.skip_1st_line) if self.commit: session.commit()
def run(self): """ 2008-08-19 """ db = Stock_250kDB(drivername=self.drivername, username=self.db_user, password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema) db.setup(create_tables=False) session = db.session session.begin() import MySQLdb mysql_conn = MySQLdb.connect(db=self.dbname, host='banyan.usc.edu', user = self.db_user, passwd = self.db_passwd) mysql_curs = mysql_conn.cursor() from pymodule import get_gene_symbol2gene_id_set gene_symbol2gene_id_set = get_gene_symbol2gene_id_set(mysql_curs, 3702, table='genome.gene_symbol2id', upper_case_gene_symbol=1) #3702 is At's tax id reader = csv.reader(open(self.input_fname), delimiter=self.delimiter) reader.next() counter = 0 success_counter = 0 gene_id_pathway_id_set = Set() for row in reader: gene_symbol = row[0].upper() pathway_id = int(row[1]) gene_id_set = gene_symbol2gene_id_set.get(gene_symbol) if gene_id_set==None: sys.stderr.write("Linking to gene id failed for %s. No such gene_symbol, %s, in gene_symbol2gene_id_set.\n"%(gene_symbol,gene_symbol)) elif len(gene_id_set)==1: gene_id = list(gene_id_set)[0] gene_id_pathway_id_set.add((gene_id, pathway_id)) success_counter += 1 elif len(gene_id_set)>1: sys.stderr.write("Too many gene_ids: %s, %s.\n"%(gene_symbol, gene_id_set)) elif len(gene_id_set)==0: sys.stderr.write("Linking to gene id failed for %s. There is gene_symbol, %s, in gene_symbol2gene_id_set but it's empty.\n"%(gene_symbol, gene_symbol)) else: sys.stderr.write("not supposed to happen: original_name=%s, gene_symbol=%s, gene_id_set=%s\n."%(gene_symbol, gene_symbol, gene_id_set)) counter += 1 for gene_id, pathway_id in gene_id_pathway_id_set: rows = FTGene.query.filter_by(gene_id=gene_id).filter_by(pathway_id=pathway_id) if rows.count()>0: row = rows.first() sys.stderr.write('gene_id %s, pathway_id %s already in db with id=%s.\n'%(gene_id, pathway_id, row.id)) continue ft_gene = FTGene(gene_id=gene_id, pathway_id=pathway_id) session.save_or_update(ft_gene) session.flush() if self.commit: session.commit()
def run(self): """ 2008-08-19 """ if self.debug: import pdb pdb.set_trace() db = Stock_250kDB(drivername=self.drivername, username=self.db_user, password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema) db.setup(create_tables=False) import MySQLdb mysql_conn = MySQLdb.connect(db=self.dbname, host='banyan.usc.edu', user = self.db_user, passwd = self.db_passwd) mysql_curs = mysql_conn.cursor() from pymodule import get_gene_symbol2gene_id_set gene_symbol2gene_id_set = get_gene_symbol2gene_id_set(mysql_curs, 3702, table='genome.gene_symbol2id', upper_case_gene_symbol=1) #3702 is At's tax id session = db.session session.begin() self.putGeneListIntoDb(self.input_fname, self.list_type_id, self.list_type_name, gene_symbol2gene_id_set, db, self.skip_1st_line) if self.commit: session.commit()
def run(self): if self.debug: import pdb pdb.set_trace() import MySQLdb mysql_conn = MySQLdb.connect(db=self.dbname, host='banyan.usc.edu', user=self.db_user, passwd=self.db_passwd) mysql_curs = mysql_conn.cursor() from pymodule import get_gene_symbol2gene_id_set gene_symbol2gene_id_set = get_gene_symbol2gene_id_set( mysql_curs, 3702, table='genome.gene_symbol2id', upper_case_gene_symbol=1) #3702 is At's tax id from variation.src.DrawSNPRegion import DrawSNPRegion DrawSNPRegion_ins = DrawSNPRegion(db_user=self.db_user, db_passwd=self.db_passwd, hostname=self.hostname, database=self.dbname,\ input_fname='/tmp/dumb', output_dir='/tmp', debug=0) #input_fname and output_dir are just random stuff gene_annotation = DrawSNPRegion_ins.dealWithGeneAnnotation( self.gene_annotation_picklef, cls_with_db_args=DrawSNPRegion_ins) self.improveTAIRGeneGFF(self.input_fname, gene_symbol2gene_id_set, gene_annotation, self.output_fname)
def run(self): """ 2008-08-19 """ db = Stock_250kDB(drivername=self.drivername, username=self.db_user, password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema) db.setup(create_tables=False) session = db.session session.begin() import MySQLdb mysql_conn = MySQLdb.connect(db=self.dbname, host='banyan.usc.edu', user=self.db_user, passwd=self.db_passwd) mysql_curs = mysql_conn.cursor() from pymodule import get_gene_symbol2gene_id_set gene_symbol2gene_id_set = get_gene_symbol2gene_id_set( mysql_curs, 3702, table='genome.gene_symbol2id', upper_case_gene_symbol=1) #3702 is At's tax id reader = csv.reader(open(self.input_fname), delimiter=self.delimiter) reader.next() counter = 0 success_counter = 0 gene_id_pathway_id_set = Set() for row in reader: gene_symbol = row[0].upper() pathway_id = int(row[1]) gene_id_set = gene_symbol2gene_id_set.get(gene_symbol) if gene_id_set == None: sys.stderr.write( "Linking to gene id failed for %s. No such gene_symbol, %s, in gene_symbol2gene_id_set.\n" % (gene_symbol, gene_symbol)) elif len(gene_id_set) == 1: gene_id = list(gene_id_set)[0] gene_id_pathway_id_set.add((gene_id, pathway_id)) success_counter += 1 elif len(gene_id_set) > 1: sys.stderr.write("Too many gene_ids: %s, %s.\n" % (gene_symbol, gene_id_set)) elif len(gene_id_set) == 0: sys.stderr.write( "Linking to gene id failed for %s. There is gene_symbol, %s, in gene_symbol2gene_id_set but it's empty.\n" % (gene_symbol, gene_symbol)) else: sys.stderr.write( "not supposed to happen: original_name=%s, gene_symbol=%s, gene_id_set=%s\n." % (gene_symbol, gene_symbol, gene_id_set)) counter += 1 for gene_id, pathway_id in gene_id_pathway_id_set: rows = FTGene.query.filter_by(gene_id=gene_id).filter_by( pathway_id=pathway_id) if rows.count() > 0: row = rows.first() sys.stderr.write( 'gene_id %s, pathway_id %s already in db with id=%s.\n' % (gene_id, pathway_id, row.id)) continue ft_gene = FTGene(gene_id=gene_id, pathway_id=pathway_id) session.save_or_update(ft_gene) session.flush() if self.commit: session.commit()