def main(dataN='TCGA_GBM', query):
con, cursor = mymysql.connectDB(db='tcga1')
geneN, altType, feature, cutoff = query.split(':')
cursor.execute('create temporary table t1 select samp_id pId, % value from %s where gene_sym="%s"' % \
(altTypeH[altType][1],altTypeH[altType][0],geneN))
cursor.execute('select value from t1')
valueL = [v for (v, ) in cursor.fetchall()]
l = len(valueL)
recordL = mymysql.dictSelect(
"SELECT pId,days_followup time,if(days_death is not null,1,0) event,%s value \
FROM clinical join %s on pId=samp_id and gene_sym='%s'" %
(altTypeH[altType][1], altTypeH[altType][0], geneN), cursor)
threshold = (mymath.percentile(valueL, cutoff[0]),
mymath.percentile(valueL, 100 - cutoff[1]))
outFile = open('/var/www/html/survival/survival.mvc', 'w')
colN = ['pId', 'time', 'event', 'value', 'label', 'priority']
outFile.write('\t'.join(colN) + '\n')
for r in recordL:
if r['value'] < threshold[0]:
label = '"%s %s < B%s%% (%.2f)"' % (geneN, altType, cutoff[0],
threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > T%s%% (%.2f)"' % (geneN, altType, cutoff[1],
threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN, altType)
priority = '9'
outFile.write(
'%s\t%s\t%s\t%s\t%s\t%s\n' %
(r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system(
'Rscript distribution.r /var/www/html/survival/survival.mvc &> /var/www/html/survival/error_distr.txt'
)
ret2 = os.system(
'Rscript survival.r /var/www/html/survival/survival.mvc &> /var/www/html/survival/error_surv.txt'
)
return ret1 != 0 or ret2 != 0
def main(dataN='TCGA_GBM', endPoint='death', geneN='MGMT', altType='methyl', cutoff=(50,50)):
colN = ['pId','time','event','value','label','priority']
con,cursor = mymysql.connectDB(db='tcga1')
cursor.execute('select samp_id from mutation_normal where gene_symL="IDH1" and ch_aa like "%sR132%s"' % ('%','%'))
idh1 = [x[0] for x in cursor.fetchall()]
recordL = mymysql.dictSelect("SELECT pId,days_followup time,if(days_death is not null,1,0) event,%s value \
FROM clinical join %s on pId=samp_id and %s='%s'" % (altTypeH[altType][1],altTypeH[altType][0],altTypeH[altType][2],geneN), cursor)
recordL2=[]
for i in range(len(recordL)):
if recordL[i]['pId'] in idh1:
continue
else:
recordL2.append(recordL[i])
recordL = recordL2
# for r in recordL:
# if r['pId'] in idh1:
# recordL.remove(r)
valueL = [r['value'] for r in recordL]
l = len(valueL)
threshold = (mymath.percentile(valueL,cutoff[0]), mymath.percentile(valueL,100-cutoff[1]))
outFile = open('/var/www/html/tmp/survival.mvc','w')
outFile.write('\t'.join(colN)+'\n')
for r in recordL:
if r['value'] < threshold[0]:
label = '"%s %s < B%s%% (%.2f)"' % (geneN,altType,cutoff[0],threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > T%s%% (%.2f)"' % (geneN,altType,cutoff[1],threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN,altType)
priority = '9'
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system('Rscript distribution.r /var/www/html/tmp/survival.mvc &> /var/www/html/tmp/error_surv.txt')
ret2 = os.system('Rscript survival.r /var/www/html/tmp/survival.mvc png &>> /var/www/html/tmp/error_surv.txt')
os.system('Rscript survival.r /var/www/html/tmp/survival.mvc pdf &>> /var/www/html/tmp/error_surv.txt')
return ret1!=0 or ret2!=0
def main(dataN='TCGA_GBM', endPoint='death', geneN='EGFR', altType='2-7', cutoff=(50,50)):
colN = ['pId','time','event','value','label','priority']
con,cursor = mymysql.connectDB(db='tcga1')
cursor.execute('create temporary table t1 select distinct samp_id pId from splice_normal')
cursor.execute('create temporary table t2 \
select pId, nReads/(nReads+nReads_w1) af from t1 left join splice_skip_AF on pId=samp_id and gene_sym="EGFR" and delExons like "%2-7%"')
cursor.execute('update t2 set af=0 where af is null')
recordL = mymysql.dictSelect("SELECT pId,days_followup time,if(days_death is not null,1,0) event, af value \
FROM clinical join t2 using (pId)", cursor)
# valueL = [r['value'] for r in recordL]
# l = len(valueL)
threshold = (0.01,0.01)
outFile = open('/var/www/html/tmp/survival.mvc','w')
outFile.write('\t'.join(colN)+'\n')
for r in recordL:
r['value'] = float(r['value'])
if r['value'] < threshold[0]:
label = '"%s %s < %.2f"' % (geneN,altType,threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > %.2f"' % (geneN,altType,threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN,altType)
priority = '9'
if r['pId'] not in CIMP:
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system('Rscript distribution.r /var/www/html/tmp/survival.mvc png &> /var/www/html/tmp/error_distr.txt')
ret2 = os.system('Rscript survival.r /var/www/html/tmp/survival.mvc png &> /var/www/html/tmp/error_surv.txt')
return ret1!=0 or ret2!=0
def main(dataN='TCGA_GBM', query):
con,cursor = mymysql.connectDB(db='tcga1')
geneN,altType,feature,cutoff = query.split(':')
cursor.execute('create temporary table t1 select samp_id pId, % value from %s where gene_sym="%s"' % \
(altTypeH[altType][1],altTypeH[altType][0],geneN))
cursor.execute('select value from t1')
valueL = [v for (v,) in cursor.fetchall()]; l = len(valueL)
recordL = mymysql.dictSelect("SELECT pId,days_followup time,if(days_death is not null,1,0) event,%s value \
FROM clinical join %s on pId=samp_id and gene_sym='%s'" % (altTypeH[altType][1],altTypeH[altType][0],geneN), cursor)
threshold = (mymath.percentile(valueL,cutoff[0]), mymath.percentile(valueL,100-cutoff[1]))
outFile = open('/var/www/html/survival/survival.mvc','w')
colN = ['pId','time','event','value','label','priority']
outFile.write('\t'.join(colN)+'\n')
for r in recordL:
if r['value'] < threshold[0]:
label = '"%s %s < B%s%% (%.2f)"' % (geneN,altType,cutoff[0],threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > T%s%% (%.2f)"' % (geneN,altType,cutoff[1],threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN,altType)
priority = '9'
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system('Rscript distribution.r /var/www/html/survival/survival.mvc &> /var/www/html/survival/error_distr.txt')
ret2 = os.system('Rscript survival.r /var/www/html/survival/survival.mvc &> /var/www/html/survival/error_surv.txt')
return ret1!=0 or ret2!=0
def main(dataN='TCGA_GBM', endPoint='death', geneN='MGMT', altType='methyl', cutoff=(50,50)):
colN = ['pId','time','event','value','label','priority']
con,cursor = mymysql.connectDB(db='tcga1')
recordL = mymysql.dictSelect("SELECT pId,days_followup time,if(days_death is not null,1,0) event,%s value \
FROM clinical join %s on pId=samp_id and %s='%s'" % (altTypeH[altType][1],altTypeH[altType][0],altTypeH[altType][2],geneN), cursor)
valueL = [r['value'] for r in recordL]
l = len(valueL)
threshold = (mymath.percentile(valueL,cutoff[0]), mymath.percentile(valueL,100-cutoff[1]))
outFile = open('/var/www/html/tmp/survival.mvc','w')
outFile.write('\t'.join(colN)+'\n')
for r in recordL:
if r['value'] < threshold[0]:
label = '"%s %s < B%s%% (%.2f)"' % (geneN,altType,cutoff[0],threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > T%s%% (%.2f)"' % (geneN,altType,cutoff[1],threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN,altType)
priority = '9'
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system('Rscript distribution.r /var/www/html/tmp/survival.mvc &> /var/www/html/tmp/error_surv.txt')
ret2 = os.system('Rscript survival.r /var/www/html/tmp/survival.mvc png &>> /var/www/html/tmp/error_surv.txt')
os.system('Rscript survival.r /var/www/html/tmp/survival.mvc pdf &>> /var/www/html/tmp/error_surv.txt')
return ret1!=0 or ret2!=0
def main(dataN='TCGA_GBM',
endPoint='death',
geneN='MGMT',
altType='methyl',
cutoff=(50, 50)):
colN = ['pId', 'time', 'event', 'value', 'label', 'priority']
con, cursor = mymysql.connectDB(db='tcga1')
cursor.execute(
'select samp_id from mutation_normal where gene_symL="IDH1" and ch_aa like "%sR132%s"'
% ('%', '%'))
idh1 = [x[0] for x in cursor.fetchall()]
recordL = mymysql.dictSelect(
"SELECT pId,days_followup time,if(days_death is not null,1,0) event,%s value \
FROM clinical join %s on pId=samp_id and %s='%s'" %
(altTypeH[altType][1], altTypeH[altType][0], altTypeH[altType][2],
geneN), cursor)
recordL2 = []
for i in range(len(recordL)):
if recordL[i]['pId'] in idh1:
continue
else:
recordL2.append(recordL[i])
recordL = recordL2
# for r in recordL:
# if r['pId'] in idh1:
# recordL.remove(r)
valueL = [r['value'] for r in recordL]
l = len(valueL)
threshold = (mymath.percentile(valueL, cutoff[0]),
mymath.percentile(valueL, 100 - cutoff[1]))
outFile = open('/var/www/html/tmp/survival.mvc', 'w')
outFile.write('\t'.join(colN) + '\n')
for r in recordL:
if r['value'] < threshold[0]:
label = '"%s %s < B%s%% (%.2f)"' % (geneN, altType, cutoff[0],
threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > T%s%% (%.2f)"' % (geneN, altType, cutoff[1],
threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN, altType)
priority = '9'
outFile.write(
'%s\t%s\t%s\t%s\t%s\t%s\n' %
(r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system(
'Rscript distribution.r /var/www/html/tmp/survival.mvc &> /var/www/html/tmp/error_surv.txt'
)
ret2 = os.system(
'Rscript survival.r /var/www/html/tmp/survival.mvc png &>> /var/www/html/tmp/error_surv.txt'
)
os.system(
'Rscript survival.r /var/www/html/tmp/survival.mvc pdf &>> /var/www/html/tmp/error_surv.txt'
)
return ret1 != 0 or ret2 != 0
def main(dataN='TCGA_GBM',
endPoint='death',
geneN='MGMT',
altType='methyl',
cutoff=(50, 50)):
colN = ['pId', 'time', 'event', 'value', 'label', 'priority']
con, cursor = mymysql.connectDB(db='tcga1')
recordL = mymysql.dictSelect(
"SELECT pId,days_followup time,if(days_death is not null,1,0) event,%s value \
FROM clinical join %s on pId=samp_id and %s='%s'" %
(altTypeH[altType][1], altTypeH[altType][0], altTypeH[altType][2],
geneN), cursor)
valueL = [r['value'] for r in recordL]
l = len(valueL)
threshold = (mymath.percentile(valueL, cutoff[0]),
mymath.percentile(valueL, 100 - cutoff[1]))
outFile = open('/var/www/html/tmp/survival.mvc', 'w')
outFile.write('\t'.join(colN) + '\n')
for r in recordL:
if r['value'] < threshold[0]:
label = '"%s %s < B%s%% (%.2f)"' % (geneN, altType, cutoff[0],
threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > T%s%% (%.2f)"' % (geneN, altType, cutoff[1],
threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN, altType)
priority = '9'
outFile.write(
'%s\t%s\t%s\t%s\t%s\t%s\n' %
(r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system(
'Rscript distribution.r /var/www/html/tmp/survival.mvc &> /var/www/html/tmp/error_surv.txt'
)
ret2 = os.system(
'Rscript survival.r /var/www/html/tmp/survival.mvc png &>> /var/www/html/tmp/error_surv.txt'
)
os.system(
'Rscript survival.r /var/www/html/tmp/survival.mvc pdf &>> /var/www/html/tmp/error_surv.txt'
)
return ret1 != 0 or ret2 != 0
def main(dataN='TCGA_GBM',
endPoint='death',
geneN='EGFR',
altType='2-7',
cutoff=(50, 50)):
colN = ['pId', 'time', 'event', 'value', 'label', 'priority']
con, cursor = mymysql.connectDB(db='tcga1')
cursor.execute(
'create temporary table t1 select distinct samp_id pId from splice_normal'
)
cursor.execute('create temporary table t2 \
select pId, nReads/(nReads+nReads_w1) af from t1 left join splice_skip_AF on pId=samp_id and gene_sym="EGFR" and delExons like "%2-7%"'
)
cursor.execute('update t2 set af=0 where af is null')
recordL = mymysql.dictSelect(
"SELECT pId,days_followup time,if(days_death is not null,1,0) event, af value \
FROM clinical join t2 using (pId)", cursor)
# valueL = [r['value'] for r in recordL]
# l = len(valueL)
threshold = (0.01, 0.01)
outFile = open('/var/www/html/tmp/survival.mvc', 'w')
outFile.write('\t'.join(colN) + '\n')
for r in recordL:
r['value'] = float(r['value'])
if r['value'] < threshold[0]:
label = '"%s %s < %.2f"' % (geneN, altType, threshold[0])
priority = '1'
elif r['value'] >= threshold[1]:
label = '"%s %s > %.2f"' % (geneN, altType, threshold[1])
priority = '2'
else:
label = '"%s %s Middle"' % (geneN, altType)
priority = '9'
if r['pId'] not in CIMP:
outFile.write(
'%s\t%s\t%s\t%s\t%s\t%s\n' %
(r['pId'], r['time'], r['event'], r['value'], label, priority))
outFile.close()
ret1 = os.system(
'Rscript distribution.r /var/www/html/tmp/survival.mvc png &> /var/www/html/tmp/error_distr.txt'
)
ret2 = os.system(
'Rscript survival.r /var/www/html/tmp/survival.mvc png &> /var/www/html/tmp/error_surv.txt'
)
return ret1 != 0 or ret2 != 0