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)
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)
def main(datFileN, server='smc1', dbN='CancerSCAN'):
mybasic.add_module_path(['NGS/mutation', 'Integration'])
import vep_batch, makeDB_mutation_rxsq
print mysetting.CSmutDir + '/*CS'
vep_batch.main(glob(mysetting.CSmutDir + '/*CS'),
postfixL=[
'.mutect_filter.vcf', '.mutect_single_filter.vcf',
'.indels_filter.vcf', '.indels_single_filter.vcf'
],
fork=True)
os.system(
'cat %s/*CS/*filter_vep.dat | /usr/bin/python %s/Integration/prepDB_mutation_cancerscan.py > %s'
% (mysetting.CSmutDir, mysetting.SRC_HOME, datFileN))
mymysql.reset_table(tableN='mutation_cs',
dataFileN=datFileN,
user=mysetting.mysqlH[server]['user'],
passwd=mysetting.mysqlH[server]['passwd'],
db=dbN,
host=mysetting.mysqlH[server]['host'])
(con,
cursor) = mymysql.connectDB(user=mysetting.mysqlH[server]['user'],
passwd=mysetting.mysqlH[server]['passwd'],
db=dbN,
host=mysetting.mysqlH[server]['host'])
sampNL = filter(lambda x: os.path.isdir(mysetting.CSmutDir + '/' + x),
os.listdir(mysetting.CSmutDir))
for sampN in sampNL:
id = '_'.join(sampN.split('_')[:-2])
postfix = sampN.split('_')[-2]
if postfix == 'B':
continue
if postfix != 'T':
id = '%s_%s' % (id, postfix)
cursor.execute(
'''DELETE FROM sample_tag WHERE samp_id="%s" AND tag="XSeq_CS"''' %
id)
cursor.execute(
'''INSERT INTO sample_tag SET samp_id="%s",tag="XSeq_CS"''' % id)
def main(datFileN, server='smc1', dbN='CancerSCAN'):
mybasic.add_module_path(['NGS/mutation','Integration'])
import vep_batch, makeDB_mutation_rxsq
print mysetting.CSmutDir+'/*CS'
vep_batch.main(glob(mysetting.CSmutDir+'/*CS'), postfixL=['.mutect_filter.vcf','.mutect_single_filter.vcf','.indels_filter.vcf','.indels_single_filter.vcf'], fork=True)
os.system('cat %s/*CS/*filter_vep.dat | /usr/bin/python %s/Integration/prepDB_mutation_cancerscan.py > %s' % (mysetting.CSmutDir, mysetting.SRC_HOME, datFileN))
mymysql.reset_table(tableN='mutation_cs', dataFileN=datFileN, user=mysetting.mysqlH[server]['user'],passwd=mysetting.mysqlH[server]['passwd'],db=dbN,host=mysetting.mysqlH[server]['host'])
(con, cursor) = mymysql.connectDB(user=mysetting.mysqlH[server]['user'],passwd=mysetting.mysqlH[server]['passwd'],db=dbN,host=mysetting.mysqlH[server]['host'])
sampNL = filter(lambda x: os.path.isdir(mysetting.CSmutDir+'/'+x), os.listdir(mysetting.CSmutDir))
for sampN in sampNL:
id = '_'.join(sampN.split('_')[:-2])
postfix = sampN.split('_')[-2]
if postfix == 'B':
continue
if postfix != 'T':
id = '%s_%s' % (id, postfix)
cursor.execute('''DELETE FROM sample_tag WHERE samp_id="%s" AND tag="XSeq_CS"''' % id)
cursor.execute('''INSERT INTO sample_tag SET samp_id="%s",tag="XSeq_CS"''' % id)