" REFERENCE_SEQUENCE=",
opts.refseq,
" WINDOW_SIZE=",
opts.windowsize,
" MINIMUM_GENOME_FRACTION=",
opts.mingenofrac,
" INPUT=",
opts.input,
" OUTPUT=",
tempout,
" TMP_DIR=",
opts.tmp_dir,
" CHART_OUTPUT=",
temppdf,
" SUMMARY_OUTPUT=",
temptab,
" VALIDATION_STRINGENCY=LENIENT",
]
process = Popen("".join(cl), shell=True, stderr=standard_fd, stdout=standard_fd, cwd=output_folder)
return_value = process.wait()
standard_fd.close()
fixPicardOutputs(
tempout=temptab,
output_dir=output_folder,
log_file=opts.log_file,
html_output=os.path.join(output_folder, opts.html_output),
progname=progname,
cl=cl,
)
def picVal(opts=None):
"""
called with sam so no need to convert
"""
assert opts <> None
killme = string.punctuation + string.whitespace
trantab = string.maketrans(killme, '_' * len(killme))
title = opts.title.translate(trantab)
tempout = os.path.join(opts.output_dir, 'rgPicardValidate.out')
temptab = os.path.join(opts.output_dir, 'rgPicardValidate.xls')
opts.log_file = opts.log or os.path.join(opts.output_dir,
'rgPicardValidate_%s.log' % title)
# Create output folder and save our R script in there.
stf = open(opts.log_file, 'w')
sortedfile = None
if verbose:
print '# opts.ignore', opts.ignore, ' opts.sortme=', opts.sortme
if opts.sortme:
fd, sortedfile = tempfile.mkstemp(suffix='rgcleansam.sorted.bam')
if opts.datatype == 'sam': # need to work with a bam
tempbam = samToBam(opts.input, opts.outdir)
pysam.sort(tempbam, sortedfile)
else: # is already bam
pysam.sort(opts.input, sortedfile)
cl = [
'java -Xmx', opts.maxjheap, ' -jar ', opts.jar, ' O=', tempout,
' TMP_DIR=', opts.tmp_dir
]
if verbose:
print '# cl so far', cl
if opts.sortme:
cl.append(' I=%s' % sortedfile)
else:
cl.append(' I=%s' % opts.input)
if opts.maxoutput == '0':
opts.maxoutput = '65535'
cl.append(' MAX_OUTPUT=%s' % opts.maxoutput)
if opts.ignore[0] <> 'None': # picard error values to ignore
cl += [' IGNORE=%s' % x for x in opts.ignore if x <> 'None']
if opts.bisulphite.lower() <> 'false':
cl.append(' IS_BISULFITE_SEQUENCED=true')
if opts.refseq <> '':
cl += [
' R=%s' % opts.refseq,
]
s1 = ' '.join(['"%s"' % x for x in cl])
s = '## rgPicardValidate.py about to Popen:\n%s\n' % s1
stf.write(s)
if verbose:
print s
pefilename = os.path.join(opts.output_dir,
'rgPicardValidate_%s.errors' % title)
picerrors = open(pefilename, 'w')
process = Popen(''.join(cl),
shell=True,
stderr=picerrors,
stdout=picerrors,
cwd=opts.output_dir)
return_value = process.wait()
picerrors.close()
pe = open(pefilename, 'r').readlines()
stf.write('## got %d rows - first few =%s\n' %
(len(pe), '\n'.join(pe[:5])))
if opts.dryrun <> 'dryrun': # want to run cleansam
if opts.dryrun == 'sam':
outformat = 'sam'
newsam = opts.sam
elif opts.dryrun == 'bam':
outformat = 'bam'
newsam = opts.bam
cleanSam(insam=opts.input,
newsam=newsam,
picardErrors=pe,
outformat=outformat,
sortme=opts.sortme)
stf.close()
fixPicardOutputs(tempout=tempout,
output_dir=opts.output_dir,
log_file=opts.log_file,
html_output=opts.html_output,
progname=progname,
cl=cl,
transpose=False)
if opts.sortme:
os.unlink(sortedfile)
if opts.datatype == 'sam': # was converted
os.unlink(tempbam) # temporary
stderr=picerrors,
stdout=picerrors,
cwd=opts.output_dir)
return_value = process.wait()
picerrors.close()
pe = open(pefilename, 'r').readlines()
stf.write('## got %d rows - first few =%s\n' %
(len(pe), '\n'.join(pe[:5])))
if opts.dryrun <> 'dryrun': # want to run cleansam
if opts.dryrun == 'sam':
outformat = 'sam'
newsam = opts.sam
elif opts.dryrun == 'bam':
outformat = 'bam'
newsam = opts.bam
cleanSam(insam=opts.input,
newsam=newsam,
picardErrors=pe,
outformat=outformat,
sortme=opts.sortme)
stf.close()
fixPicardOutputs(tempout=tempout,
output_dir=opts.output_dir,
log_file=opts.log_file,
html_output=opts.html_output,
progname=progname,
cl=cl,
transpose=False)
if opts.sortme:
os.unlink(sortedfile)
# Create output folder and save our R script in there.
standard_fd = open(opts.log_file, 'w')
cl = [
'java -Xmx', opts.maxjheap, ' -jar ', opts.jar, ' REFERENCE_SEQUENCE=',
opts.refseq, ' WINDOW_SIZE=', opts.windowsize,
' MINIMUM_GENOME_FRACTION=', opts.mingenofrac, ' INPUT=', opts.input,
' OUTPUT=', tempout, ' TMP_DIR=', opts.tmp_dir, ' CHART_OUTPUT=',
temppdf, ' SUMMARY_OUTPUT=', temptab, ' VALIDATION_STRINGENCY=LENIENT'
]
process = Popen(''.join(cl),
shell=True,
stderr=standard_fd,
stdout=standard_fd,
cwd=opts.output_dir)
return_value = process.wait()
cl = 'mogrify -format jpg -resize x500 %s' % (
temppdf) # make the jpg for fixPicardOutputs to find
process = Popen(cl,
shell=True,
stderr=standard_fd,
stdout=standard_fd,
cwd=opts.output_dir)
return_value = process.wait()
standard_fd.close()
fixPicardOutputs(tempout=temptab,
output_dir=opts.output_dir,
log_file=opts.log_file,
html_output=opts.html_output,
progname=progname,
cl=cl)
else:
bedToPicInterval(opts.target, targetf)
tempout = os.path.join(opts.output_dir,'rgPicardHsMetrics.out')
opts.log_file = opts.log or os.path.join(opts.output_dir, '%s.log' % title)
sfd = open(opts.log_file, 'w')
cl = ['java -Xmx',opts.maxjheap,' -jar ',opts.jar,
' BAIT_INTERVALS=',baitf,' TARGET_INTERVALS=',
targetf,' INPUT=',os.path.abspath(opts.input),
' OUTPUT=',tempout,
' VALIDATION_STRINGENCY=LENIENT', ' TMP_DIR=',opts.tmp_dir
]
process = Popen(''.join(cl), shell=True, stderr=sfd, stdout=sfd, cwd=opts.output_dir)
return_value = process.wait()
sfd.close()
fixPicardOutputs(tempout=tempout, output_dir=opts.output_dir,
log_file=opts.log_file,
html_output=os.path.join(opts.output_dir, opts.html_output),
progname=progname,
cl=cl)
destination = os.path.join(output_folder, new_filename)
shutil.copy(os.path.abspath(opts.refseq), destination)
opts.refseq = destination
standard_fd = open(opts.log_file, 'w')
cl = [
'java -Xmx', opts.maxjheap, ' -jar ', opts.jar, ' REFERENCE_SEQUENCE=',
os.path.abspath(opts.refseq), ' ASSUME_SORTED=', opts.assume_sorted,
''.join([' ADAPTER_SEQUENCE=%s' % x
for x in opts.adapters]), ' IS_BISULFITE_SEQUENCED=',
opts.bisulphite, ' MAX_INSERT_SIZE=', opts.maxinsert, ' INPUT=',
os.path.abspath(opts.input), ' OUTPUT=', tempout,
' VALIDATION_STRINGENCY=LENIENT', ' TMP_DIR=', opts.tmp_dir
]
process = Popen(''.join(cl),
shell=True,
stderr=standard_fd,
stdout=standard_fd,
cwd=opts.output_dir)
return_value = process.wait()
standard_fd.close()
fixPicardOutputs(tempout=tempout,
output_dir=opts.output_dir,
log_file=opts.log_file,
html_output=os.path.join(opts.output_dir,
opts.html_output),
progname=progname,
cl=cl)
print s
pefilename = os.path.join(opts.output_dir, 'rgPicardValidate_%s.errors' % title)
picerrors = open(pefilename,'w')
process = Popen(''.join(cl), shell=True, stderr=picerrors, stdout=picerrors, cwd=opts.output_dir)
return_value = process.wait()
picerrors.close()
pe = open(pefilename,'r').readlines()
stf.write('## got %d rows - first few =%s\n' % (len(pe), '\n'.join(pe[:5])))
if opts.dryrun <> 'dryrun': # want to run cleansam
if opts.dryrun == 'sam':
outformat = 'sam'
newsam = opts.sam
elif opts.dryrun == 'bam':
outformat = 'bam'
newsam = opts.bam
cleanSam(insam=opts.input, newsam=newsam, picardErrors=pe,outformat=outformat,sortme=opts.sortme)
stf.close()
fixPicardOutputs(tempout=tempout,output_dir=opts.output_dir,
log_file=opts.log_file,html_output=opts.html_output,progname=progname,cl=cl,transpose=False)
if opts.sortme:
os.unlink(sortedfile)
def picVal(opts=None):
"""
called with sam so no need to convert
"""
assert opts <> None
killme = string.punctuation + string.whitespace
trantab = string.maketrans(killme,'_'*len(killme))
title = opts.title.translate(trantab)
tempout = os.path.join(opts.output_dir,'rgPicardValidate.out')
temptab = os.path.join(opts.output_dir,'rgPicardValidate.xls')
opts.log_file = opts.log or os.path.join(opts.output_dir, 'rgPicardValidate_%s.log' % title)
# Create output folder and save our R script in there.
stf = open(opts.log_file, 'w')
sortedfile=None
if verbose:
print '# opts.ignore',opts.ignore,' opts.sortme=',opts.sortme
if opts.sortme:
fd,sortedfile = tempfile.mkstemp(suffix='rgcleansam.sorted.bam')
if opts.datatype == 'sam': # need to work with a bam
tempbam = samToBam(opts.input,opts.outdir)
pysam.sort(tempbam,sortedfile)
else: # is already bam
pysam.sort(opts.input,sortedfile)
cl = ['java -Xmx',opts.maxjheap,' -jar ',opts.jar,' O=',tempout,' TMP_DIR=',opts.tmp_dir]
if verbose:
print '# cl so far',cl
if opts.sortme:
cl.append(' I=%s' % sortedfile)
else:
cl.append(' I=%s' % opts.input)
if opts.maxoutput == '0':
opts.maxoutput = '65535'
cl.append(' MAX_OUTPUT=%s' % opts.maxoutput)
if opts.ignore[0] <> 'None': # picard error values to ignore
cl += [' IGNORE=%s' % x for x in opts.ignore if x <> 'None']
if opts.bisulphite.lower() <> 'false':
cl.append(' IS_BISULFITE_SEQUENCED=true')
if opts.refseq <> '':
cl += [' R=%s' % opts.refseq,]
s1 = ' '.join(['"%s"' % x for x in cl])
s = '## rgPicardValidate.py about to Popen:\n%s\n' % s1
stf.write(s)
if verbose:
print s
pefilename = os.path.join(opts.output_dir, 'rgPicardValidate_%s.errors' % title)
picerrors = open(pefilename,'w')
process = Popen(''.join(cl), shell=True, stderr=picerrors, stdout=picerrors, cwd=opts.output_dir)
return_value = process.wait()
picerrors.close()
pe = open(pefilename,'r').readlines()
stf.write('## got %d rows - first few =%s\n' % (len(pe), '\n'.join(pe[:5])))
if opts.dryrun <> 'dryrun': # want to run cleansam
if opts.dryrun == 'sam':
outformat = 'sam'
newsam = opts.sam
elif opts.dryrun == 'bam':
outformat = 'bam'
newsam = opts.bam
cleanSam(insam=opts.input, newsam=newsam, picardErrors=pe,outformat=outformat,sortme=opts.sortme)
stf.close()
fixPicardOutputs(tempout=tempout,output_dir=opts.output_dir,
log_file=opts.log_file,html_output=opts.html_output,progname=progname,cl=cl,transpose=False)
if opts.sortme:
os.unlink(sortedfile)
if opts.datatype == 'sam': # was converted
os.unlink(tempbam) # temporary
except:
pass
title = opts.namejob.translate(trantab)
tempout = os.path.join(opts.output_dir,'rgPicardGCBiasMetrics.out')
temppdf = os.path.join(opts.output_dir,'rgPicardGCBiasMetrics.pdf')
temptab = os.path.join(opts.output_dir,'rgPicardGCBiasMetrics.xls')
opts.log_file = opts.log or os.path.join(opts.output_dir, '%s.log' % title)
# Create output folder and save our R script in there.
standard_fd = open(opts.log_file, 'w')
cl = ['java -Xmx',opts.maxjheap,' -jar ',opts.jar,' REFERENCE_SEQUENCE=',opts.refseq,' WINDOW_SIZE=',opts.windowsize,
' MINIMUM_GENOME_FRACTION=',opts.mingenofrac,' INPUT=',opts.input,' OUTPUT=',tempout,' TMP_DIR=',opts.tmp_dir,
' CHART_OUTPUT=',temppdf,' SUMMARY_OUTPUT=',temptab,' VALIDATION_STRINGENCY=LENIENT']
process = Popen(''.join(cl), shell=True, stderr=standard_fd, stdout=standard_fd, cwd=opts.output_dir)
return_value = process.wait()
cl = 'mogrify -format jpg -resize x500 %s' % (temppdf) # make the jpg for fixPicardOutputs to find
process = Popen(cl, shell=True, stderr=standard_fd, stdout=standard_fd, cwd=opts.output_dir)
return_value = process.wait()
standard_fd.close()
fixPicardOutputs(tempout=temptab,output_dir=opts.output_dir,
log_file=opts.log_file,html_output=opts.html_output,progname=progname,cl=cl)
