Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

Appendix B
# BaFL probe cleansing from the DataCleansing_6_26.py file
def RunCleanse(usr, pswd, db, logfile, lwr=200, uppr=20000, rgr=4):
Driver(usr, pswd, db, logfile, lwr=200, uppr=20000)
DriverSNP(usr, pswd, db, logfile)
DriverXH(usr, pswd, db, logfile)
DriverBioPhy(usr, pswd, db, logfile)
DriverFNL(usr, pswd, db, logfile, rgr)
def exec_mapping(usr, pswd, db, tables, msk, msk_tab, fp, lwr, uppr):
cur, conn= make_connect(usr, pswd, db)
exp=get_exp(usr, pswd, db)
notes='known probe sequence info within linear range'
map=get_masking(tables, msk, msk_tab)
chip_info = " as select
known_seq_biophysical.probeset_id,known_seq_biophysical.probe_index,kno
wn_seq_biophysical.pm_mm_other, known_seq_biophysical.probeseq,"
k=0
#print 'Map length ', len(map), map[k]
pid_tbles=[]
for i in tables:
tmp=msk[map[k]]+'_pid'
trl= "CREATE table
"+tmp+chip_info+i+".x,"+i+".y,"+i+".signalrawintensity from
"+i+",known_seq_biophysical where known_seq_biophysical.x = "+i+".x and
known_seq_biophysical.y = "+i+".y and (signalrawintensity >= "+
str(lwr) +" and signalrawintensity =0)"
print trl
cur.execute(trl)
conn.commit()
#print trl, '\n\n'
fp.write('\tTable '), fp.write(tmp), fp.write('
created.\n')
pid_tbles.append(tmp)
cur, conn=UpdateWorkReg(cur, conn, tmp, exp,
'linear_range', usr, i, 'known_seq_biophysical', notes)
k+=1
onto='select * from '+tmp
cur.execute(onto)
desc=cur.description
conn.close()
fp=UpdateOntology2(usr, pswd, db, desc, exp, 'linear_range',
'_pid', notes, str(lwr)+', '+str(uppr), fp)
fp.close()
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