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

fp.write('\tTable '), fp.write(msk[k]+ '_BioP '),
fp.write(' created.\n')
pid_tbles.append(msk[k]+ '_BioP')
trl='drop table tmp'
cur.execute(trl)
conn.commit()
cur, conn=UpdateWorkReg(cur, conn, msk[k]+'_BioP', exp,
'biophysical_filter', usr, msk[k]+'_XH', 'known_seq_biophysical',
notes)
k+=1
onto='select * from '+msk[k-1]+'_BioP'
cur.execute(onto)
desc=cur.description
conn.close()
fp=UpdateOntology2(usr, pswd, db, desc, exp,
'biophysical_filter', '_BioP', notes, '', fp)
fp.close()
def DriverBioPhy(usr, pswd, db, logfile):
# first step when combines chip and cel info
cur, conn= make_connect(usr, pswd, db)
msk, msk_tab, Lmsk, state=get_mask2(cur)
#print len(msk), len(tables), len(msk_tab)
t = datetime.datetime.now()
EpochSeconds=time.mktime(t.timetuple())
now = datetime.datetime.fromtimestamp(EpochSeconds)
fp=open(logfile, 'a')
fp.write('\n')
fp.write('Biophysical filters:\n')
conn.close()
BioPhy_filter(usr, pswd, db, msk, msk_tab, fp)
def Fnl_filter(usr, pswd, db, msk, msk_tab, fp, rgr):
cur, conn= make_connect(usr, pswd, db)
exp=get_exp(usr, pswd, db)
notes='probesets w/ statistical rigor'
k=0
#print 'Map length ', len(map), map[k]
pid_tbles=[]
#fp=open(logfile,'a')
for i in msk:
trl= 'create table tmp as select count(*), probeset_id from
'
trl=trl+ msk[k]+ '_BioP group by probeset_id having
count(*) >='+str(rgr)
cur.execute(trl)
conn.commit()
trl= 'create table ' +msk[k]+'_SR'+str(rgr)+' as select '
trl=trl+msk[k]+'_BioP.* from '+msk[k]+'_BioP inner join tmp
on (tmp.probeset_id = ' +msk[k]+'_BioP.probeset_id) order by '+
msk[k]+'_BioP.probeset_id, '+msk[k]+'_BioP.probe_index'
cur.execute(trl)
conn.commit()
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