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): if self.debug: import pdb pdb.set_trace() db = Stock_250kDB.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() snps_context_wrapper = GeneListRankTest.dealWithSnpsContextWrapper(self.snps_context_picklef, self.min_distance, self.get_closest) gene_annotation = DrawSNPRegion.dealWithGeneAnnotation(self.gene_annotation_picklef) snp_info = DrawSNPRegion.getSNPInfo(db) snp_annotation_short_name2id = self.getSNPAnnotationShortName2id() self._constructSNPAnnotation(session, snp_info, snps_context_wrapper, gene_annotation, snp_annotation_short_name2id) if self.commit: session.flush() session.commit()
def db_connect(self):
"""
2010-1-15
pass "cls_with_db_args=self" to DrawSNPRegion.dealWithGeneAnnotation()
2009-12-09
add db_user, db_passwd to MySQLdb.connect()
2008-12-16
add gene_annotation_picklef
2008-02-01
read the data in dialog_db_connect and establish the connections to two databases
"""
sys.stderr.write("Database Connecting ...")
self.drivername = 'mysql'
self.hostname = self.entry_mysql_hostname.get_text()
self.dbname = self.entry_mysql_dbname.get_text()
self.db_user = self.xml.get_widget("entry_db_user").get_text()
self.db_passwd = self.xml.get_widget("entry_db_passwd").get_text()
import MySQLdb
try:
self.mysql_conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user=self.db_user, passwd=self.db_passwd)
self.mysql_curs = self.mysql_conn.cursor()
self.db = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname)
self.db.setup(create_tables=False)
self.session = self.db.session
except:
sys.stderr.write('DB connection error: %s\n'%repr(sys.exc_info()))
traceback.print_exc()
if not self.gene_annotation:
gene_annotation_picklef = self.entry_gene_annotation_picklef.get_text()
self.gene_annotation = DrawSNPRegion.dealWithGeneAnnotation(gene_annotation_picklef, cls_with_db_args=self)
#2010-1-13 for postgresql. commented out
#hostname = self.entry_postgres_hostname.get_text()
#dbname = self.entry_postgres_dbname.get_text()
#schema = self.entry_postgres_schema.get_text()
#from annot.bin.codense.common import db_connect #2008-12-16 don't need postgres conn anymore
#self.postgres_conn, self.postgres_curs = db_connect(hostname, dbname, schema)
sys.stderr.write("Done.\n")
def run(self): if self.debug: import pdb pdb.set_trace() db = Stock_250kDB.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() snps_context_wrapper = GeneListRankTest.dealWithSnpsContextWrapper(self.snps_context_picklef, self.min_distance, \ self.get_closest) gene_annotation = DrawSNPRegion.dealWithGeneAnnotation(self.gene_annotation_picklef, tax_id=self.tax_id, \ cls_with_db_args=self) snp_info = DrawSNPRegion.getSNPInfo(db) snp_annotation_short_name2id = self.getSNPAnnotationShortName2id() self._constructSNPAnnotation(session, snp_info, snps_context_wrapper, gene_annotation, snp_annotation_short_name2id) if self.commit: session.flush() 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)
