本文整理汇总了Python中mymysql.connectDB函数的典型用法代码示例。如果您正苦于以下问题：Python connectDB函数的具体用法？Python connectDB怎么用？Python connectDB使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了connectDB函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: main
def main(geneN1, geneN2, altType1='rpkm', altType2='rpkm', dset='tcga1'):
tblN1,valN1,featN1,lab1 = altTypeH[altType1]
tblN2,valN2,featN2,lab2 = altTypeH[altType2]
con,cursor = mymysql.connectDB(db=dset)
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()]
ret1 = os.system('''(echo "SELECT t1.samp_id,t1.%s %s,t2.%s %s FROM %s t1, %s t2 where t1.%s='%s' and t2.%s='%s' and t1.samp_id=t2.samp_id" | mysql %s -u cancer --password=cancer > /var/www/html/tmp/correlation.txt) &> /var/www/html/tmp/correaltion.err''' % \
(valN1,geneN1, valN2,geneN2, tblN1,tblN2, featN1,geneN1, featN2,geneN2, dset))
f = open('/var/www/html/tmp/correlation.txt')
fo = open('/var/www/html/tmp/correlation_idh1.txt','w')
for line in f:
(sId, t1, t2) = line[:-1].split('\t')
if sId in idh1:
fo.write('%s\t%s\t%s\t%s\n' % (sId,t1,t2,'mut'))
else:
fo.write('%s\t%s\t%s\t%s\n' % (sId,t1,t2,'na'))
f.close()
fo.close()
ret2 = os.system('Rscript correlation_idh1.r "%s" "%s" "%s" png &>> /var/www/html/tmp/correaltion.err' % (dsetH[dset],lab1,lab2))
return ret1!=0 or ret2!=0
开发者ID:SMC1，项目名称:JK1，代码行数:29，代码来源:correlation_idh1.py
示例2: main
def main(inDir, outDir, pbs=False, server='smc1'):
inFileNL = os.listdir(inDir)
inFileNL = filter(lambda x: re.match('.*\.ngCGH', x), inFileNL)
print 'Files: %s' % inFileNL
(con, cursor) = mymysql.connectDB(user=mysetting.mysqlH[server]['user'], passwd=mysetting.mysqlH[server]['passwd'], db='ircr1', host=mysetting.mysqlH[server]['host'])
for inFileN in inFileNL:
sampN = re.match('(.*)\.ngCGH', inFileN).group(1)
(sid, tag) = re.match('(.*)_(T.{,2}.*)_[STKN]{2}\.ngCGH', inFileN).groups()
if tag != 'T':
sid = '%s_%s' % (sid, tag)
cursor.execute('SELECT tumor_frac FROM xsq_purity WHERE samp_id="%s"' % sid)
purity = int(cursor.fetchall()[0][0])
iprefix = '%s/%s' % (inDir,sampN)
oprefix = '%s/%s' % (outDir,sampN)
cmd = '/usr/bin/python %s/NGS/copynumber/cn_corr.py -i %s.ngCGH -o %s.corr.ngCGH -p %s' % (mysetting.SRC_HOME, iprefix, oprefix, purity)
log = '%s.cn_corr.qlog' % (oprefix)
print cmd
if pbs:
os.system('echo "%s" | qsub -N %s -o %s -j oe' % (cmd, sampN, log))
else:
os.system('(%s) &> %s' % (cmd, log))
开发者ID:SMC1，项目名称:JK1，代码行数:26，代码来源:cn_corr_batch.py
示例3: prep_somatic_new
def prep_somatic_new(outFileN, server='smc1', dbN='ircr1'):
## run VEP
vep_batch.main(glob('/EQL3/pipeline/somatic_mutation/*S'), postfixL=['.mutect_rerun_filter.vcf','.mutect_filter.vcf','.mutect_pair_filter.vcf','.indels_pair_filter.vcf'], fork=True)
## make table
DIR='/EQL3/pipeline/somatic_mutation'
cmd = 'cat %s/*/*filter_vep.dat | /usr/bin/python %s/Integration/prepDB_mutation_xsq2mut_tmp.py > %s' % (DIR, mysetting.SRC_HOME, outFileN)
os.system(cmd)
## update tag
sidL = map(lambda x: x.rstrip(), os.popen('cut -f 1 %s | sort | uniq' % outFileN).readlines())
(con, cursor) = mymysql.connectDB(user=mysetting.mysqlH[server]['user'],passwd=mysetting.mysqlH[server]['passwd'],db=dbN,host=mysetting.mysqlH[server]['host'])
for sid in sidL:
cursor.execute('SELECT samp_id,tag FROM sample_tag WHERE samp_id="%s" AND tag LIKE "XSeq_%%"' % sid)
results = cursor.fetchall()
if len(results)>0:
if len(results)>1:
sys.stderr.write('Duplication in sample_tag: %s\n' % sid)
sys.exit(1)
else:
old_tag = results[0][1]
new_tag = '%s,N' % old_tag
cursor.execute('UPDATE sample_tag SET samp_id="%s", tag="%s" WHERE samp_id="%s" AND tag="%s"' % (sid,new_tag, sid,old_tag))
else:
cursor.execute('INSERT INTO sample_tag SET samp_id="%s", tag="XSeq_SS,N"' % sid)
开发者ID:SMC1，项目名称:JK1，代码行数:25，代码来源:post_xsq2mut.py
示例4: post_rsq2eiJunc
def post_rsq2eiJunc(dirN, server='smc1', dbN='ihlee_test', sampL=[]):
(con, cursor) = mymysql.connectDB(user=mysqlH[server]['user'],passwd=mysqlH[server]['passwd'],db=dbN,host=mysqlH[server]['host'])
sampNL = filter(lambda x: os.path.isdir(dirN + '/' + x), os.listdir(dirN))
for sampN in sampNL:
baseDir = dirN + '/' + sampN
sid = sampN[:-4].replace('.','_').replace('-','_') ## RNASeq sample has '***_RSq'
if sampL != [] and sid not in sampL:
continue
print sampN, sid
## make sure to update sample_tag that this sample has RNA-Seq
cursor.execute('SELECT * FROM sample_tag WHERE samp_id="%s" AND tag="RNA-Seq"' % sid)
results = cursor.fetchall()
if len(results) < 1:
cursor.execute('INSERT INTO sample_tag SET samp_id="%s", tag="RNA-Seq"' % sid)
ei_dat = glob('%s/%s*ei.dat' % (baseDir, sampN))[0]
if dbN in ['ihlee_test','ircr1']:
splice_eiJunc_txt = '%s/eiJunc/splice_eiJunc_%s_ft.txt' % (BASE, sampN)
else:
splice_eiJunc_txt = '%s/splice_eiJunc_%s_ft.txt' % (baseDir, sampN)
ei_junc_filter.main(overlap=10, minNReads=1, inFileN=ei_dat, outFileN=splice_eiJunc_txt)
if dbN in ['ihlee_test','ircr1']:
splice_eiJunc_dat = '%s/eiJunc/splice_eiJunc_%s.dat' % (BASE, sampN)
else:
splice_eiJunc_dat = '%s/splice_eiJunc_%s.dat' % (baseDir, sampN)
prepDB_splice_eiJunc.main(minNReads=1, sampNamePat=RSQPattern, geneList=[], inFileN=splice_eiJunc_txt, outFileN=splice_eiJunc_dat)
cursor.execute('DELETE FROM splice_eiJunc WHERE samp_id="%s"' % sid)
cursor.execute('LOAD DATA LOCAL INFILE "%s" IGNORE INTO TABLE splice_eiJunc' % splice_eiJunc_dat)
makeDB_splice_AF.eiJunc(dbN=dbN, cursor=cursor)
开发者ID:SMC1，项目名称:JK1，代码行数:28，代码来源:post_rsq2other.py
示例5: post_rsq2fusion
def post_rsq2fusion(dirN, server='smc1', dbN='ihlee_test', sampL=[]):
(con, cursor) = mymysql.connectDB(user=mysqlH[server]['user'],passwd=mysqlH[server]['passwd'],db=dbN,host=mysqlH[server]['host'])
sampNL = filter(lambda x: os.path.isdir(dirN + '/' + x), os.listdir(dirN))
for sampN in sampNL:
baseDir = dirN + '/' + sampN
sid = sampN[:-4].replace('.','_').replace('-','_') ## RNASeq sample has '***_RSq'
if sampL != [] and sid not in sampL:
continue
print sampN, sid
## make sure to update sample_tag that this sample has RNA-Seq
cursor.execute('SELECT * FROM sample_tag WHERE samp_id="%s" AND tag="RNA-Seq"' % sid)
results = cursor.fetchall()
if len(results) < 1:
cursor.execute('INSERT INTO sample_tag SET samp_id="%s", tag="RNA-Seq"' % sid)
fusion_report_annot = glob('%s/%s*_splice_transloc_annot1.report_annot.txt' % (baseDir, sampN))[0]
if dbN in ['ihlee_test','ircr1']:
splice_fusion_txt = '%s/fusion/splice_fusion_%s.txt' % (BASE, sampN)
else:
splice_fusion_txt = '%s/splice_fusion_%s.txt' % (baseDir, sampN)
fusion_summarize.fusion_summarize_s(inputFileN=fusion_report_annot, minNPos=1, outFileN=splice_fusion_txt)
if dbN in ['ihlee_test','ircr1']:
splice_fusion_dat = '%s/fusion/splice_fusion_%s.dat' % (BASE, sampN)
else:
splice_fusion_dat = '%s/splice_fusion_%s.dat' % (baseDir, sampN)
prepDB_splice_fusion.main(inGctFileName=splice_fusion_txt, minNPos=1, sampNamePat=RSQPattern, geneList=[], outFileN=splice_fusion_dat)
cursor.execute('DELETE FROM splice_fusion WHERE samp_id="%s"' % sid)
cursor.execute('LOAD DATA LOCAL INFILE "%s" IGNORE INTO TABLE splice_fusion' % splice_fusion_dat)
cursor.execute('DELETE FROM splice_fusion WHERE gene_sym1 LIKE "HLA-%" AND gene_sym2 LIKE "HLA-%"')
makeDB_splice_AF.fusion(dbN=dbN, cursor=cursor)
开发者ID:SMC1，项目名称:JK1，代码行数:30，代码来源:post_rsq2other.py
示例6: main
def main(outFileName,dbNL,dTypeL,outDirName,outFileN):
for dbN in dbNL:
(con,cursor) = mymysql.connectDB(db=dbN)
if dbN == 'ircr1':
cursor.execute('create temporary table t_recur select distinct samp_id from sample_tag where substring(tag,1,6)="pair_P"')
elif dbN == 'tcga1':
cursor.execute('create temporary table t_recur select distinct samp_id from sample_tag where tag="Recur"')
cursor.execute('SELECT distinct loc,geneName FROM tcga1.methyl_pId where platform="Infinium27k"')
results1 = cursor.fetchall()
for dType in dTypeL:
for (loc,geneN) in results1:
outFile = open(outFileName,'w')
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % ('dbT','dType','geneN','PR','sId','val','loc'))
for PR in ('P','R'):
cursor.execute('select pId,%s from %s where platform="Infinium27k" and loc="%s" and geneName="%s" and pId %s in (select samp_id from t_recur)' % (dTypeH[dType][1],dTypeH[dType][0],loc,geneN,'not' if PR=='P' else ''))
results = cursor.fetchall()
for (sId,val) in results:
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (dbH[dbN],dType,geneN,PR,sId,val,loc))
outFile.close()
os.system('Rscript %s/PrimRecur/unpaired_gene_methyl_ks.r %s %s &>> %s/error_kstest.txt' % (mysetting.SRC_HOME,outDirName,outFileN,outDirName))
con.close()
开发者ID:SMC1，项目名称:JK1，代码行数:35，代码来源:df_unpaired_gene_methyl.py
示例7: post_s_rsq2expr
def post_s_rsq2expr(baseDir, server='smc1', dbN='ihlee_test'):
sampN = baseDir.split('/')[-1]
sid = sampN[:-4].replace('-','_').replace('.','_') ##drop '_RSq'
if dbN in ['ihlee_test','ircr1']:
gctFileN = '/EQL1/NSL/RNASeq/results/expression/%s.gct' % sampN
datFileN = '/EQL1/NSL/RNASeq/results/expression/%s.dat' % sampN
else:
gctFileN = '%s/%s.gct' % (baseDir, sampN)
datFileN = '%s/%s.dat' % (baseDir, sampN)
print sampN, gctFileN
rpkm_process.rpkm_process(inputDirN=baseDir, filePattern='*.rpkm', sampRegex='(.*)_RSq\.rpkm', outputFileN=gctFileN)
## prep
prepDB_rpkm_gene_expr.main(inGctFileName=gctFileN, geneList=[], samplePrefix='', outDatFileName=datFileN)
## import
(con, cursor) = mymysql.connectDB(user=mysqlH[server]['user'],passwd=mysqlH[server]['passwd'],db=dbN,host=mysqlH[server]['host'])
cursor.execute('DELETE FROM rpkm_gene_expr WHERE samp_id="%s"' % sid)
cursor.execute('LOAD DATA LOCAL INFILE "%s" INTO TABLE rpkm_gene_expr' % datFileN)
cursor.execute('DROP VIEW IF EXISTS rpkm_gene_expr_lg2')
cursor.execute('CREATE VIEW rpkm_gene_expr_lg2 AS SELECT samp_id,gene_sym,log2(rpkm+1) AS lg2_rpkm FROM rpkm_gene_expr')
## make sure to update sample_tag that this sample has RNA-Seq
cursor.execute('SELECT * FROM sample_tag WHERE samp_id="%s" AND tag="RNA-Seq"' % sid)
results = cursor.fetchall()
if len(results) < 1:
cursor.execute('INSERT INTO sample_tag SET samp_id="%s", tag="RNA-Seq"' % sid)
##draw boxplot
boxplot_expr_cs_gene.main(sid, '/EQL1/NSL/RNASeq/results/expression')
开发者ID:SMC1，项目名称:JK1，代码行数:28，代码来源:post_rsq2expr.py
示例8: main
def main(dbN='ircr1', cursor=None):
if cursor == None:
(con,cursor) = mymysql.connectDB(db=dbN)
cursor.execute('drop table if exists mutation_rxsq')
cursor.execute('create temporary table t_m as \
select n.samp_id,n.chrom,n.chrSta,n.chrEnd,n.ref,n.alt,n.n_nReads_ref,n.n_nReads_alt,n.nReads_ref,n.nReads_alt,r.r_nReads_ref,r.r_nReads_alt,n.strand,n.gene_symL,n.ch_dna,n.ch_aa,n.ch_type,n.cosmic,n.mutsig \
from mutation_normal n left join mutation_rsq r \
on n.samp_id = r.samp_id and n.chrom=r.chrom and n.chrSta=r.chrSta and n.ref=r.ref and n.alt=r.alt \
union \
select r.samp_id,r.chrom,r.chrSta,r.chrEnd,r.ref,r.alt,n.n_nReads_ref,n.n_nReads_alt,n.nReads_ref,n.nReads_alt,r.r_nReads_ref,r.r_nReads_alt,r.strand,r.gene_symL,r.ch_dna,r.ch_aa,r.ch_type,r.cosmic,r.mutsig \
from mutation_normal n right join mutation_rsq r \
on n.samp_id = r.samp_id and n.chrom=r.chrom and n.chrSta=r.chrSta and n.ref=r.ref and n.alt=r.alt')
cursor.execute('create table mutation_rxsq as \
select * from (select * from t_m order by ch_dna desc) as i group by samp_id,chrom,chrSta,ref,alt,ch_aa')
cursor.execute('update mutation_rxsq set r_nReads_ref = 0, r_nReads_alt = 0 where r_nReads_ref is null')
cursor.execute('update mutation_rxsq set n_nReads_ref = 0, n_nReads_alt = 0 where n_nReads_ref is null')
cursor.execute('update mutation_rxsq set nReads_ref = 0, nReads_alt = 0 where nReads_ref is null')
cursor.execute('alter table mutation_rxsq add index (samp_id,gene_symL)')
cursor.execute('alter table mutation_rxsq add index (samp_id,chrom,chrSta,chrEnd)')
cursor.execute('alter table mutation_rxsq add index (samp_id,chrom,chrSta,ref,alt)')
cursor.execute('alter table mutation_rxsq add index (samp_id,chrom,chrSta,chrEnd,ref,alt)')
cursor.execute('drop temporary table if exists t_m')
开发者ID:SMC1，项目名称:JK1，代码行数:28，代码来源:makeDB_mutation_rxsq.py
示例9: main
def main(inDir, outDir, cnDir, pbs=False, server='smc1'):
inFileNL = os.listdir(inDir)
inFileNL = filter(lambda x: not re.match('(.*)\.union_pos\.mutect$', x), filter(lambda x: re.match('(.*)\.mutect$', x), inFileNL))
print 'Files: %s' % inFileNL
(con, cursor) = mymysql.connectDB(user=mysetting.mysqlH[server]['user'], passwd=mysetting.mysqlH[server]['passwd'], db='ircr1', host=mysetting.mysqlH[server]['host'])
for inFileN in inFileNL:
sampN = re.match('(.*)\.mutect', inFileN).group(1)
(sid, postfix) = re.match('(.*)_(T.{,2})_[STKN]{2}\.mutect', inFileN).groups()
if postfix != 'T':
sid = '%s_%s' % (sid, postfix)
cursor.execute('SELECT tumor_frac FROM xsq_purity WHERE samp_id="%s"' % sid)
result = cursor.fetchall()
if len(result) > 0 and result[0][0] != 'ND':
purity = int(result[0][0])
iprefix = '%s/%s' % (inDir, sampN)
oprefix = '%s/%s' % (outDir, sampN)
segFile = '%s/%s/%s.ngCGH.seg' % (cnDir, sampN, sampN)
if os.path.isfile(segFile) and not os.path.isfile('%s.mutect_cl.dat' % (oprefix)):
cmd = '/usr/bin/python %s/NGS/mutation/mut_clonality.py -s %s -i %s.mutect -o %s.mutect_cl.dat -p %s' % (mysetting.SRC_HOME, segFile, iprefix, oprefix, purity)
log = '%s.mutect_cl.log' % (oprefix)
if pbs:
os.system('echo "%s" | qsub -N %s -o %s -j oe' % (cmd, sampN, log))
else:
os.system('(%s) &> %s' % (cmd, log))
else:
print "Missing copy number segmentation file!"
sys.exit(1)
开发者ID:SMC1，项目名称:JK1，代码行数:31，代码来源:mut_clonality_batch.py
示例10: main
def main(outFileName):
(con,cursor) = mymysql.connectDB(db='ircr1')
outFile = open(outFileName,'w')
cursor.execute('select distinct samp_id from sample_tag where substring(tag,1,6)="pair_R" and samp_id!="S520" and samp_id!="S042"')
sIdL_prim = [x for (x,) in cursor.fetchall()]
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % ('dType','geneN','sId_p','sId_r','val_p','val_r'))
for dType in dTypeL:
for geneN in geneL:
for sId_p in sIdL_prim:
(tbl,col_name,col_val) = dTypeH[dType]
cursor.execute('select samp_id from sample_tag where tag="pair_P:%s"' % sId_p)
(sId_r,) = cursor.fetchone()
cursor.execute('select %s from %s where %s="%s" and samp_id="%s"' % (col_val,tbl,col_name,geneN,sId_p))
r_p = cursor.fetchone()
cursor.execute('select %s from %s where %s="%s" and samp_id="%s"' % (col_val,tbl,col_name,geneN,sId_r))
r_r = cursor.fetchone()
if r_p and r_r:
outFile.write('%s\t%s\t%s\t%s\t%.2f\t%.2f\n' % (dType,geneN,sId_p,sId_r,r_p[0],r_r[0]))
outFile.close()
con.close()
开发者ID:SMC1，项目名称:JK1，代码行数:33，代码来源:df_paired_pathway.py
示例11: main
def main():
con,cursor = mymysql.connectDB(db='tcga1')
cursor.execute('SELECT distinct platform,loc FROM methyl_pId')
results1 = cursor.fetchall()
output = []
for (plat,loc) in results1:
#cursor.execute('select fraction,z_score from methyl_pId, array_gene_expr where platform="%s" and loc="%s" and gene_sym="MGMT" and pId=samp_id' % (plat,loc))
cursor.execute('select fraction,log2(rpkm+1) from methyl_pId, rpkm_gene_expr where platform="%s" and loc="%s" and gene_sym="MGMT" and pId=samp_id' % (plat,loc))
results2 = cursor.fetchall()
methyl,expr = zip(*results2)
r = numpy.corrcoef(methyl,expr)[0,1]
output.append((plat,loc,len(methyl),r))
output.sort(lambda x,y: cmp(y[-1],x[-1]))
for (plat,loc,n,r) in output:
print '%s\t%s\t%s\t%.2f' % (plat,loc,n,r)
开发者ID:SMC1，项目名称:JK1，代码行数:25，代码来源:select_methyl_loc.py
示例12: post_xsq2cn
def post_xsq2cn(outFileN, platform='', server='smc1', dbN='ircr1'):
if platform == 'CS':
cmd = 'cat %s/*/*%s.cn_gene.dat | /usr/bin/python %s/Integration/prepDB_xsq_cn.py > %s' % (mysetting.CScnaDir,platform, mysetting.SRC_HOME, outFileN)
else:
cmd = 'cat %s/*/*%s.cn_gene.dat | /usr/bin/python %s/Integration/prepDB_xsq_cn.py > %s' % (mysetting.wxsCNADir,platform, mysetting.SRC_HOME, outFileN)
os.system(cmd)
if platform == 'SS':
tableN = 'xsq_cn'
elif platform == 'CS':
tableN = 'cs_cn'
else:
sys.stderr.write('illegal platform name: %s' % platform)
sys.exit(1)
mymysql.reset_table(tableN=tableN, dataFileN=outFileN, user=mysetting.mysqlH[server]['user'],passwd=mysetting.mysqlH[server]['passwd'],db=dbN, host=mysetting.mysqlH[server]['host'])
## add samp_id if missing
(con, cursor) = mymysql.connectDB(user=mysetting.mysqlH[server]['user'], passwd=mysetting.mysqlH[server]['passwd'], db=dbN, host=mysetting.mysqlH[server]['host'])
cursor.execute('SELECT DISTINCT samp_id FROM %s' % tableN)
sIdL = [x for (x,) in cursor.fetchall()]
cursor.execute('SELECT DISTINCT samp_id FROM sample_tag WHERE tag like "XSeq_%s%%"' % platform)
refL = [x for (x,) in cursor.fetchall()]
for sid in sIdL:
if sid not in refL:
pl = platform
cursor.execute('INSERT INTO sample_tag SET samp_id="%s", tag="XSeq_%s"' % (sid, pl))
开发者ID:SMC1，项目名称:JK1，代码行数:26，代码来源:post_xsq2other.py
示例13: main
def main(locFileName):
con,cursor = mymysql.connectDB(db='tcga1')
locFile = open(locFileName)
cursor.execute('drop table if exists methyl_gene')
for line in locFile:
(plat, gN, loc, n, r) = line[:-1].split('\t')
if r != '-nan' and float(r) <= -0.25:
cursor.execute('create temporary table t_methyl as \
select * from methyl where geneName="%s" and platform="%s" and loc="%s"' % (gN,plat,loc))
cursor.execute('alter table t_methyl add column r float, add column n smallint unsigned')
cursor.execute('update t_methyl set n=%s, r=%s' % (int(n),float(r)))
try:
cursor.execute('create table methyl_gene as \
select platform,pId,geneName,loc,sum(fraction)/count(fraction) fraction, n, r from t_methyl group by pId')
except:
cursor.execute('insert into methyl_gene \
select platform,pId,geneName,loc,sum(fraction)/count(fraction) fraction, n, r from t_methyl group by pId')
cursor.execute('drop table t_methyl')
cursor.execute('alter table methyl_gene add index (geneName)')
cursor.execute('alter table methyl_gene add index (pId)')
开发者ID:SMC1，项目名称:JK1，代码行数:31，代码来源:makeDB_methyl_gene.py
示例14: main
def main():
con,cursor = mymysql.connectDB(db='tcga1')
cursor.execute('create temporary table t_EGFR as \
select platform,pId,geneName,loc,sum(fraction)/count(fraction) fraction from tcga1.methyl where TN="T" and geneName = "EGFR" \
group by platform, pId, loc')
cursor.execute('alter table t_EGFR add index (geneName)')
cursor.execute('alter table t_EGFR add index (pId)')
cursor.execute('SELECT distinct platform,loc FROM t_EGFR')
results1 = cursor.fetchall()
output = []
for (plat,loc) in results1:
#cursor.execute('select fraction,z_score from methyl_pId, array_gene_expr where platform="%s" and loc="%s" and gene_sym="MGMT" and pId=samp_id' % (plat,loc))
cursor.execute('select fraction,log2(rpkm+1) from t_EGFR, rpkm_gene_expr where platform="%s" and loc="%s" and gene_sym="EGFR" and pId=samp_id' % (plat,loc))
results2 = cursor.fetchall()
methyl,expr = zip(*results2)
r = numpy.corrcoef(methyl,expr)[0,1]
output.append((plat,loc,len(methyl),r))
output.sort(lambda x,y: cmp(y[-1],x[-1]))
for (plat,loc,n,r) in output:
print '%s\t%s\t%s\t%.3f' % (plat,loc,n,r)
开发者ID:SMC1，项目名称:JK1，代码行数:32，代码来源:select_methyl_loc_EGFR.py
示例15: main
def main(outFileName,dbNL,dTypeL,geneNL):
outFile = open(outFileName,'w')
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % ('dbT','dType','geneN','PR','sId','val'))
for dbN in dbNL:
(con,cursor) = mymysql.connectDB(db=dbN)
if dbN == 'ircr1':
cursor.execute('create temporary table t_recur select distinct samp_id from sample_tag where substring(tag,1,6)="pair_P"')
elif dbN == 'tcga1':
cursor.execute('create temporary table t_recur select distinct samp_id from sample_tag where tag="Recur"')
for dType in dTypeL:
for geneN in geneNL:
for PR in ('P','R'):
cursor.execute('select samp_id,%s from %s where gene_sym="%s" and samp_id %s in (select samp_id from t_recur)' % (dTypeH[dType][1],dTypeH[dType][0],geneN,'not' if PR=='P' else ''))
results = cursor.fetchall()
for (sId,val) in results:
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (dbH[dbN],dType,geneN,PR,sId,val))
con.close()
outFile.close()
开发者ID:SMC1，项目名称:JK1，代码行数:30，代码来源:df_unpaired_gene.py
示例16: main
def main(geneN,dType,dbN='ircr1',outFileDir=None):
if outFileDir:
outFile = open('%s/%s_%s_%s_paired.dst2' % (outFileDir,geneN,dType,dbH[dbN]),'w')
else:
outFile = sys.stdout
(con,cursor) = mymysql.connectDB(db=dbN)
cursor.execute('select distinct samp_id from sample_tag where substring(tag,1,6)="pair_R"')
sIdL_prim = [x for (x,) in cursor.fetchall()]
vL = []; sIdL_pair = []
for sId_p in sIdL_prim:
cursor.execute('select samp_id from sample_tag where tag="pair_P:%s"' % sId_p)
(sId_r,) = cursor.fetchone()
cursor.execute('select %s from %s where gene_sym="%s" and samp_id="%s"' % (dTypeH[dType][1],dTypeH[dType][0],geneN,sId_p))
r_p = cursor.fetchone()
cursor.execute('select %s from %s where gene_sym="%s" and samp_id="%s"' % (dTypeH[dType][1],dTypeH[dType][0],geneN,sId_r))
r_r = cursor.fetchone()
if r_p and r_r:
vL.append("%.2f" % (r_r[0]-r_p[0],))
sIdL_pair.append((sId_p,sId_r))
outFile.write('%s-%s-%s\t%s\n' % (geneN,dType,dbN,len(sIdL_pair)))
outFile.write(','.join(vL)+'\n')
outFile.write(','.join(['%s_%s' % (x,y) for (x,y) in sIdL_pair])+'\n')
con.close()
开发者ID:SMC1，项目名称:JK1，代码行数:34，代码来源:dst2_paired.py
示例17: load_mutation_all
def load_mutation_all(inFileN, server='smc1', dbN='ircr1'):
(con, cursor) = mymysql.connectDB(user=mysetting.mysqlH[server]['user'],passwd=mysetting.mysqlH[server]['passwd'],db=dbN,host=mysetting.mysqlH[server]['host'])
cursor.execute('DROP TABLE IF EXISTS mutation_normal')
stmt = '''
CREATE TABLE mutation_normal (
samp_id varchar(63) NOT NULL,
chrom varchar(10) NOT NULL,
chrSta int unsigned NOT NULL,
chrEnd int unsigned NOT NULL,
ref varchar(63) NOT NULL,
alt varchar(63) NOT NULL,
n_nReads_ref mediumint unsigned NOT NULL,
n_nReads_alt mediumint unsigned NOT NULL,
nReads_ref mediumint unsigned NOT NULL,
nReads_alt mediumint unsigned NOT NULL,
strand char(1) NOT NULL,
gene_symL varchar(63),
ch_dna varchar(127),
ch_aa varchar(63),
ch_type varchar(127),
cosmic text,
mutsig text,
index (samp_id,gene_symL),
index (samp_id,chrom,chrSta,chrEnd),
index (samp_id,chrom,chrSta,ref,alt),
index (samp_id,chrom,chrSta,chrEnd,ref,alt)
)
'''
cursor.execute(stmt)
cursor.execute('CREATE TEMPORARY TABLE tmp LIKE mutation_normal')
cursor.execute('LOAD DATA LOCAL INFILE "%s" INTO TABLE tmp' % inFileN)
cursor.execute('CREATE TEMPORARY TABLE t2 SELECT tmp.samp_id,tmp.chrom,tmp.chrSta,tmp.chrEnd,tmp.ref,tmp.alt,tmp.n_nReads_ref,tmp.n_nReads_alt,tmp.nReads_ref,tmp.nReads_alt,tmp.strand,tmp.gene_symL,tmp.ch_dna,tmp.ch_aa,tmp.ch_type,cosmic.ch_aaL AS cosmic,cosmic.ch_typeL AS cosmic_type,tmp.mutsig FROM tmp LEFT JOIN cosmic ON tmp.chrom=cosmic.chrom AND tmp.chrSta=cosmic.chrSta AND tmp.chrEnd=cosmic.chrEnd AND tmp.ref=cosmic.ref AND tmp.alt=cosmic.alt AND tmp.gene_symL=cosmic.gene_symL')
cursor.execute('INSERT INTO mutation_normal SELECT samp_id,chrom,chrSta,chrEnd,ref,alt,n_nReads_ref,n_nReads_alt,nReads_ref,nReads_alt,strand,gene_symL,ch_dna,ch_aa,ch_type,"" AS cosmic,mutsig FROM t2 WHERE cosmic IS NULL')
cursor.execute('INSERT INTO mutation_normal SELECT samp_id,chrom,chrSta,chrEnd,ref,alt,n_nReads_ref,n_nReads_alt,nReads_ref,nReads_alt,strand,gene_symL,ch_dna,cosmic AS ch_aa,cosmic_type AS ch_type,cosmic,mutsig FROM t2 WHERE cosmic IS NOT NULL')
开发者ID:SMC1，项目名称:JK1，代码行数:35，代码来源:post_xsq2mut.py
示例18: make_mutation_rxsq_cs
def make_mutation_rxsq_cs(dbN='CancerSCAN', cursor=None):
if cursor == None:
(con,cursor) = mymysql.connectDB(db=dbN)
cursor.execute('''DROP TABLE IF EXISTS mutation_rxsq''')
cursor.execute('''CREATE TEMPORARY TABLE t_m AS \
SELECT n.samp_id,n.chrom,n.chrSta,n.chrEnd,n.ref,n.alt,n.n_nReads_ref,n.n_nReads_alt,n.nReads_ref,n.nReads_alt,r.r_nReads_ref,r.r_nReads_alt,ifnull(r.strand,''),n.gene_sym,n.ch_dna,n.ch_aa,n.ch_type,concat(n.cosmic,",",n.tcga) cosmic,'' mutsig \
FROM mutation_cs n LEFT JOIN mutation_rsq r \
ON n.samp_id=r.samp_id AND n.chrom=r.chrom AND n.chrSta=r.chrSta AND n.chrEnd=r.chrEnd AND n.ref=r.ref AND n.alt=r.alt\
UNION \
SELECT r.samp_id,r.chrom,r.chrSta,r.chrEnd,r.ref,r.alt,n.n_nReads_ref,n.n_nReads_alt,n.nReads_ref,n.nReads_alt,r.r_nReads_ref,r.r_nReads_alt,r.strand,r.gene_symL gene_sym,r.ch_dna,r.ch_aa,r.ch_type,r.cosmic,r.mutsig \
FROM mutation_cs n RIGHT JOIN mutation_rsq r \
ON n.samp_id=r.samp_id AND n.chrom=r.chrom AND n.chrSta=r.chrSta AND n.chrEnd=r.chrEnd AND n.ref=r.ref AND n.alt=r.alt
''')
cursor.execute('''CREATE TABLE mutation_rxsq AS \
SELECT * FROM (SELECT * FROM t_m ORDER BY ch_dna desc) AS i GROUP BY samp_id,chrom,chrSta,ref,alt,ch_aa''')
cursor.execute('''UPDATE mutation_rxsq SET r_nReads_ref=0, r_nReads_alt=0 WHERE r_nReads_ref IS NULL''')
cursor.execute('''UPDATE mutation_rxsq SET n_nReads_ref=0, n_nReads_alt=0 WHERE n_nReads_ref IS NULL''')
cursor.execute('''UPDATE mutation_rxsq SET nReads_ref=0, nReads_alt=0 WHERE nReads_ref IS NULL''')
cursor.execute('''ALTER TABLE mutation_rxsq ADD INDEX (samp_id,gene_sym)''')
cursor.execute('''ALTER TABLE mutation_rxsq ADD INDEX (samp_id,chrom,chrSta,chrEnd)''')
cursor.execute('''ALTER TABLE mutation_rxsq ADD INDEX (samp_id,chrom,chrSta,ref,alt)''')
cursor.execute('''ALTER TABLE mutation_rxsq ADD INDEX (samp_id,chrom,chrSta,chrEnd,ref,alt)''')
cursor.execute('''DROP TEMPORARY TABLE IF EXISTS t_m''')
开发者ID:SMC1，项目名称:JK1，代码行数:27，代码来源:makeDB_mutation_rxsq.py
示例19: has_acgh
def has_acgh(samp_id, dbN='ircr1'):
(con, cursor) = mymysql.connectDB(db=dbN)
cursor.execute('select count(distinct samp_id) from array_cn where samp_id="%s"' % samp_id)
if cursor.fetchone()[0] > 0:
return(True)
else:
return(False)
开发者ID:SMC1，项目名称:JK1，代码行数:7，代码来源:paired_retain.py
示例20: main
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
开发者ID:SMC1，项目名称:JK1，代码行数:59，代码来源:survival_idh1.py
注：本文中的mymysql.connectDB函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
客服电话
APP下载
官方微信
请发表评论