def checkNtvl(ci, ni):
'''Check is intervals withing the same chromosome are non overlapping
sorted increasingly by starting coordinate
'''
# print 'curr:', ci
# print 'next:', ni
if not ci:
return 0
if ci[0] == ni[0]:
if int(ci[2]) > int(ni[1]) or int(ci[1]) > int(ni[2]):
logProc.logProc(outf, outdir, ' ', 'failed', stderr_out=inf+' contains overlapping intervals or not sorted by starting coordinate '+' '.join(ci))
return 1
return 0
def checkNtvl(ci, ni):
'''Check is intervals withing the same chromosome are non overlapping
sorted increasingly by starting coordinate
'''
# print 'curr:', ci
# print 'next:', ni
if not ci:
return 0
if ci[0] == ni[0]:
if int(ci[2]) > int(ni[1]) or int(ci[1]) > int(ni[2]):
logProc.logProc(
outf,
outdir,
' ',
'failed',
stderr_out=inf +
' contains overlapping intervals or not sorted by starting coordinate '
+ ' '.join(ci))
return 1
return 0
'''
Take a union of supplied bed files.
'''
import sys, subprocess
sys.path.insert(0, '/nethome/asalomatov/projects/ppln')
import logProc
print '\nsys.args :', sys.argv
outf, outdir = sys.argv[1:3]
cmd = 'cat '+ ' '.join(sys.argv[3:]) + ' | sort -V -k1,1 -k2,2 | uniq > ' + sys.argv[1]
#print cmd
logProc.logProc(outf, outdir, cmd, 'started')
p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
if p.returncode == 0:
logProc.logProc(outf, outdir, cmd, 'finished')
else:
logProc.logProc(outf, outdir, cmd, 'failed', stderr)
'''
Filter BAMs based on criteria defined in --filter switches.
'''
import sys, subprocess
sys.path.insert(0, '/nethome/asalomatov/projects/ppln')
import logProc
nctFlag = '-nct 4'
print '\nsys.args :', sys.argv[1:]
inbam, recalibtbl, outbam, refGenome, tmpdir, gatk, outdir = sys.argv[1:]
cmd = 'java -Xms750m -Xmx2500m -XX:+UseSerialGC -Djava.io.tmpdir=%(tmpdir)s -jar %(gatk)s --read_filter BadCigar --read_filter NotPrimaryAlignment -T PrintReads -I %(inbam)s -o %(outbam)s -R %(refGenome)s -BQSR %(recalibtbl)s %(nctFlag)s'
cmd = cmd % locals()
#print cmd
logProc.logProc(outbam, outdir, cmd, 'started')
p = subprocess.Popen(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
if p.returncode == 0:
logProc.logProc(outbam, outdir, cmd, 'finished')
else:
logProc.logProc(outbam, outdir, cmd, 'failed', stderr)
'''
'''
import sys
from sets import Set
sys.path.insert(0, '/nethome/asalomatov/projects/ppln')
import logProc
if len(sys.argv) == 1:
print 'Usage:'
print sys.argv[
0], 'input.bed', 'output.bed', 'logdir', 'filter1', 'filter2', 'filter3'
N = 4
inf, outf, outdir = sys.argv[1:N]
fltrs = sys.argv[N:]
print fltrs
cmd = ' '
logProc.logProc(outf, outdir, cmd, 'started')
with open(outf, 'w') as fout:
with open(inf, 'r') as fin:
for l in fin:
ls = l.split()
if ls[3] in fltrs:
fout.write('\t'.join(ls) + '\n')
logProc.logProc(outf, outdir, cmd, 'finished')
sys.path.insert(0, "/nethome/asalomatov/projects/ppln")
import logProc
nctFlag = "-nct 4"
options = """\
-U LENIENT_VCF_PROCESSING \
--read_filter BadCigar \
--read_filter NotPrimaryAlignment \
-T PrintReads \
-I %(inbam)s \
-o %(outbam)s \
-R %(refGenome)s \
--filter_mismatching_base_and_quals \
--filter_bases_not_stored \
--filter_reads_with_N_cigar \
%(nctFlag)s"""
print "\nsys.args :", sys.argv[1:]
inbam, inbai, outbam, gatkjar, refGenome, tmpdir, outdir = sys.argv[1:]
cmd = "java -Xms750m -Xmx2500m -XX:+UseSerialGC -Djava.io.tmpdir=%(tmpdir)s -jar %(gatkjar)s " + options
cmd = cmd % locals()
# print cmd
logProc.logProc(outbam, outdir, cmd, "started")
p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
if p.returncode == 0:
logProc.logProc(outbam, outdir, cmd, "finished")
else:
logProc.logProc(outbam, outdir, cmd, "failed", stderr)
--assemble=1 \
--hapScoreThreshold=10\
--scThreshold=0.99 \
--filteredReadsFrac=0.9 \
--rmsmqThreshold=20 \
--qdThreshold=0 \
--abThreshold=0.0001 \
--minVarFreq=0.0 '''
# cmd = "%(platypus)s callVariants %(inbams)s --output=%(outfile)s --refFile=%(refGenome)s --regions=%(inregions)s "
# cmd = "%(platypus)s callVariants %(inbams)s --output=%(outfile)s --refFile=%(refGenome)s --regions=%(inregions)s %(options)s "
#--output=%(outfile)s
cmd = "%(platypus)s callVariants %(inbams)s --output=- --refFile=%(refGenome)s --regions=%(inregions)s %(options)s "
cmd += "| %(bcftools)s filter -O v --soft-filter 'PlatQualDepth' -e '(FR[0] <= 0.5 && TC < 4 && %%QUAL < 20) || (TC < 13 && %%QUAL < 10) || (FR[0] > 0.5 && TC < 4 && %%QUAL < 50)' -m '+' | %(vcflibdir)s/vcfallelicprimitives --keep-geno | %(vcflibdir)s/vcfstreamsort | %(bgzip)s -c > %(outfile)s"
print cmd
cmd = cmd % locals()
print cmd
logProc.logProc(outfile, outdir, cmd, 'started')
p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
if p.returncode == 0:
logProc.logProc(outfile, outdir, cmd, 'finished')
else:
logProc.logProc(outfile, outdir, cmd, 'failed', stderr)
except Exception as e:
logProc.logProc(outfile, outdir, ' ', 'failed', stderr_out=e.message)
raise
'''
/bioinfo/software/installs/bcbio_nextgen/150607/bin/Platypus.py callVariants --bamFiles=/mnt/scratch/asalomatov/bioppln/run11480dsPIPE03_EX_ns/work/11480.mo_SSCtest-20-re-fxgr-flr-dp-23-rlgn-rclb.bam,/mnt/scratch/asalomatov/bioppln/run11480dsPIPE03_EX_ns/work/11480.fa_SSCtest-20-re-fxgr-flr-dp-23-rlgn-rclb.bam, /mnt/scratch/asalomatov/bioppln/run11480dsPIPE03_EX_ns/work/11480.p1_SSCtest-20-re-fxgr-flr-dp-23-rlgn-rclb.bam --output=- --refFile=/bioinfo/data/bcbio_nextgen/150607/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --regions=/mnt/scratch/asalomatov/bioppln/run11480dsPIPE03_EX_ns/work/10__bin__11480-uni-mrg.bed --logF ileName=/dev/null --verbosity=1 --assemble=1 --hapScoreThreshold=10 --scThreshold=0.99 --filteredReadsFrac=0.9 --rmsmqThreshold=20 --qdThreshold=0 --abThreshold=0.0001 --minVarFreq=0.0
'''
'''
'''
import sys
from sets import Set
sys.path.insert(0, '/nethome/asalomatov/projects/ppln')
import logProc
if len(sys.argv) == 1:
print 'Usage:'
print sys.argv[0], 'input.bed', 'output.bed', 'logdir', 'filter1', 'filter2', 'filter3'
N = 4
inf, outf, outdir = sys.argv[1:N]
fltrs = sys.argv[N:]
print fltrs
cmd = ' '
logProc.logProc(outf, outdir, cmd, 'started')
with open(outf, 'w') as fout:
with open(inf, 'r') as fin:
for l in fin:
ls = l.split()
if ls[3] in fltrs:
fout.write('\t'.join(ls)+'\n')
logProc.logProc(outf, outdir, cmd, 'finished')
if int(ni[2]) - int(ci[1]) > w or ci[0] != ni[0]:
with open(fname, 'w') as fout:
fout.write('\t'.join(ci) + '\n')
ci[0] = ni[0]
ci[1] = ni[1]
ci[2] = ni[2]
return True
else:
ci[2] = ni[2]
return False
inf, outf, wdw, outdir = sys.argv[1:]
try:
logProc.logProc(outf, outdir, sys.argv[0], 'started')
curr_ntvl = []
written = True
bin_num = 0
fname = os.path.join(os.path.dirname(outf),
str(bin_num) + '__' + os.path.basename(outf))
with open(inf, 'r') as fin:
for l in fin:
ls = l.split()
if checkNtvl(curr_ntvl, ls): sys.exit(1)
written = accumNtvl(curr_ntvl, ls, int(wdw), fname)
if written:
bin_num += 1
fname = os.path.join(
os.path.dirname(outf),
str(bin_num) + '__' + os.path.basename(outf))
if int(ni[2]) - int(ci[1]) > w or ci[0] != ni[0]:
with open(fname, 'w') as fout:
fout.write('\t'.join(ci)+'\n')
ci[0] = ni[0]
ci[1] = ni[1]
ci[2] = ni[2]
return True
else:
ci[2] = ni[2]
return False
inf, outf, wdw, outdir = sys.argv[1:]
try:
logProc.logProc(outf, outdir, sys.argv[0], 'started')
curr_ntvl = []
written = True
bin_num = 0
fname = os.path.join(os.path.dirname(outf), str(bin_num)+'__'+os.path.basename(outf))
with open(inf, 'r') as fin:
for l in fin:
ls = l.split()
if checkNtvl(curr_ntvl, ls): sys.exit(1)
written = accumNtvl(curr_ntvl, ls, int(wdw), fname)
if written:
bin_num += 1
fname = os.path.join(os.path.dirname(outf), str(bin_num)+'__'+os.path.basename(outf))
if not written:
with open(fname, 'w') as fout:
fout.write('\t'.join(curr_ntvl)+'\n')
print '\nsys.args :', sys.argv[1:]
N = 8
refGenome, freebayes, vcflibdir, bgzip, outdir, outfile, inbed = sys.argv[
1:N]
fl = ' -b '
inbams = ''
for f in sys.argv[N:]:
inbams += fl + f
options = ''' \
--ploidy 2 \
--min-repeat-entropy 1'''
cmd = "%(freebayes)s %(inbams)s -f %(refGenome)s --targets %(inbed)s %(options)s "
# cmd += "| %(vcflibdir)s/vcffilter -f 'QUAL > 5' -F 'QUALlt5' -s | %(vcflibdir)s/vcfallelicprimitives | %(vcflibdir)s/vcfstreamsort | %(bgzip)s -c > %(outfile)s"
cmd += "| %(vcflibdir)s/vcffilter -f 'QUAL > 5' -F 'QUALlt5' -s | %(bgzip)s -c > %(outfile)s"
cmd = cmd % locals()
print cmd
logProc.logProc(outfile, outdir, cmd, 'started')
p = subprocess.Popen(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
if p.returncode == 0:
logProc.logProc(outfile, outdir, cmd, 'finished')
else:
logProc.logProc(outfile, outdir, cmd, 'failed', stderr)
except Exception as e:
logProc.logProc(outfile, outdir, ' ', 'failed', stderr_out=e.message)
raise
