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aggregate inteval handling fixes
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Katarzyna Sikora committed Mar 27, 2018
1 parent 090dc4c commit ef7dab9
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Showing 22 changed files with 556 additions and 331 deletions.
4 changes: 2 additions & 2 deletions BS_DMR_WGBS.py
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Expand Up @@ -38,8 +38,8 @@ def DMR_metilene(ii,sampleInfo,outfile,nthreads,metipath,my_session,logobject):
return


def clean_up_metilene(metilene_out,CpG_stats_out,sampleInfo,outdir,Rpath,pipev,my_session,logobject):
cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out + ' ' + CpG_stats_out +' ' + sampleInfo
def clean_up_metilene(metilene_out,CpG_stats_out,auxList,refG,sampleInfo,outdir,Rpath,Rlib,bedpath,pipev,my_session,logobject):
cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out +' ' + auxList + ' ' + CpG_stats_out +' ' + sampleInfo + ' ' + refG + ' "' + bedpath+'" ' + Rlib
logobject.info(cmd)
with open(os.path.join(outdir,"logs","metilene.cleanup.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","metilene.cleanup.err"),'w') as stderrF:
try:
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6 changes: 3 additions & 3 deletions BS_DMR_WGBS.py~
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Expand Up @@ -25,7 +25,7 @@ def DMR_metilene(ii,sampleInfo,outfile,nthreads,metipath,my_session,logobject):
drmaa_session = my_session,
run_locally = False,
working_directory = os.getcwd(),
job_other_options = '-p bioinfo --nodes 1=1 --mincpus='+str(nthreads))
job_other_options = '-p bioinfo --nodes=1=1 --mincpus='+str(nthreads))
stdoutF.write("".join(stdout_res))
stderrF.write("".join(stderr_res))

Expand All @@ -38,8 +38,8 @@ def DMR_metilene(ii,sampleInfo,outfile,nthreads,metipath,my_session,logobject):
return


def clean_up_metilene(metilene_out,CpG_stats_out,sampleInfo,outdir,Rpath,pipev,my_session,logobject):
cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out + ' ' + CpG_stats_out +' ' + sampleInfo
def clean_up_metilene(metilene_out,CpG_stats_out,auxList,refG,sampleInfo,outdir,Rpath,bedpath,pipev,my_session,logobject):
cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out +' ' + auxList + ' ' + CpG_stats_out +' ' + sampleInfo + ' ' + refG + ' "' + bedpath+'"'
logobject.info(cmd)
with open(os.path.join(outdir,"logs","metilene.cleanup.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","metilene.cleanup.err"),'w') as stderrF:
try:
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7 changes: 4 additions & 3 deletions BSmapWGBS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from ruffus.drmaa_wrapper import run_job, error_drmaa_job
import gzip
import subprocess
import tempfile

#####DEFINITIONS#################################################

Expand Down Expand Up @@ -36,7 +37,7 @@ def bMeth_map_reads(INfile1,INfile2,outBam,bmethpath,sampath,bamoutDir,refpathBS
sortThreads = nthreads
if nthreads > 4:
sortThreads = 4
mapcmd=bmethpath + ' bwameth.py --threads ' + str(nthreads) + ' --read-group '+ RG + ' --reference ' + refpathBS + ' ' + INfile1 + ' ' + INfile2 + ' | ' + os.path.join(sampath,'samtools') + ' sort -T ' + os.path.join('/data/extended',read_root) + ' -m 3G -@ ' + str(sortThreads) + ' -o ' + outBam
mapcmd=bmethpath + ' bwameth.py --threads ' + str(nthreads) + ' --read-group '+ RG + ' --reference ' + refpathBS + ' ' + INfile1 + ' ' + INfile2 + ' | ' + os.path.join(sampath,'samtools') + ' sort -T ' + tempfile.mkdtemp(suffix='',prefix=read_root,dir='/data/extended') + ' -m 3G -@ ' + str(sortThreads) + ' -o ' + outBam
logobject.info(mapcmd)
with open(os.path.join(bamoutDir,"logs","%s.readmap.out.log" % read_root),'w') as stdoutF, open(os.path.join(bamoutDir,"logs","%s.readmap.err.log" % read_root),'w') as stderrF:
try:
Expand Down Expand Up @@ -86,7 +87,7 @@ def BS_index_bam(INfile,sampath,bamoutDir,my_session,logobject):
def BS_rm_dupes(INfile,OUTfile,sbpath,bamoutDir,nthreads,my_session,logobject):
read_root=re.sub('.bam.bai','',os.path.basename(INfile))
INfile0=os.path.join(bamoutDir,read_root)+'.bam'
rmD_cmd=sbpath + 'sambamba_v0.6.6 markdup --remove-duplicates -t ' + str(nthreads) + ' --tmpdir /data/extended ' + INfile0 + ' ' + OUTfile + ';sleep 300'
rmD_cmd=sbpath + 'sambamba_v0.6.6 markdup --remove-duplicates -t ' + str(nthreads) + ' --tmpdir ' + tempfile.mkdtemp(suffix='',prefix='',dir='/data/extended') +' ' + INfile0 + ' ' + OUTfile + ';sleep 300'
logobject.info(rmD_cmd)
with open(os.path.join(bamoutDir,"logs","%s.rmDupes.out.log" % read_root),'w') as stdoutF, open(os.path.join(bamoutDir,"logs","%s.rmDupes.err.log" % read_root),'w') as stderrF:
try:
Expand All @@ -106,7 +107,7 @@ def BS_rm_dupes(INfile,OUTfile,sbpath,bamoutDir,nthreads,my_session,logobject):
raise
else:
logobject.info('PCR duplicate removal complete')
zeroFile(INfile)
zeroFile(INfile0)
return


Binary file modified BSmapWGBS.pyc
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7 changes: 4 additions & 3 deletions BSmapWGBS.py~
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ import logging
from ruffus.drmaa_wrapper import run_job, error_drmaa_job
import gzip
import subprocess
import tempfile

#####DEFINITIONS#################################################

Expand Down Expand Up @@ -36,7 +37,7 @@ def bMeth_map_reads(INfile1,INfile2,outBam,bmethpath,sampath,bamoutDir,refpathBS
sortThreads = nthreads
if nthreads > 4:
sortThreads = 4
mapcmd=bmethpath + ' bwameth.py --threads ' + str(nthreads) + ' --read-group '+ RG + ' --reference ' + refpathBS + ' ' + INfile1 + ' ' + INfile2 + ' | ' + os.path.join(sampath,'samtools') + ' sort -T ' + os.path.join('/data/extended',read_root) + ' -m 3G -@ ' + str(sortThreads) + ' -o ' + outBam
mapcmd=bmethpath + ' bwameth.py --threads ' + str(nthreads) + ' --read-group '+ RG + ' --reference ' + refpathBS + ' ' + INfile1 + ' ' + INfile2 + ' | ' + os.path.join(sampath,'samtools') + ' sort -T ' + tempfile.mkdtemp(suffix='',prefix=read_root,dir='/data/extended') + ' -m 3G -@ ' + str(sortThreads) + ' -o ' + outBam
logobject.info(mapcmd)
with open(os.path.join(bamoutDir,"logs","%s.readmap.out.log" % read_root),'w') as stdoutF, open(os.path.join(bamoutDir,"logs","%s.readmap.err.log" % read_root),'w') as stderrF:
try:
Expand Down Expand Up @@ -86,7 +87,7 @@ def BS_index_bam(INfile,sampath,bamoutDir,my_session,logobject):
def BS_rm_dupes(INfile,OUTfile,sbpath,bamoutDir,nthreads,my_session,logobject):
read_root=re.sub('.bam.bai','',os.path.basename(INfile))
INfile0=os.path.join(bamoutDir,read_root)+'.bam'
rmD_cmd=sbpath + 'sambamba_v0.6.6 markdup --remove-duplicates -t ' + str(nthreads) + ' --tmpdir /data/extended ' + INfile0 + ' ' + OUTfile + ';sleep 300'
rmD_cmd=sbpath + 'sambamba_v0.6.6 markdup --remove-duplicates -t ' + str(nthreads) + ' --tmpdir ' + tempfile.mkdtemp(suffix='',prefix='',dir='/data/extended') +' ' + INfile0 + ' ' + OUTfile + ';sleep 300'
logobject.info(rmD_cmd)
with open(os.path.join(bamoutDir,"logs","%s.rmDupes.out.log" % read_root),'w') as stdoutF, open(os.path.join(bamoutDir,"logs","%s.rmDupes.err.log" % read_root),'w') as stderrF:
try:
Expand All @@ -106,7 +107,7 @@ def BS_rm_dupes(INfile,OUTfile,sbpath,bamoutDir,nthreads,my_session,logobject):
raise
else:
logobject.info('PCR duplicate removal complete')
zeroFile(INfile)
zeroFile(INfile0)
return


6 changes: 3 additions & 3 deletions BSmethXT_WGBS.py
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Expand Up @@ -80,14 +80,14 @@ def methXT_POM(INfile,QCdir,OUTpfx,refG,POMpath,mextDir,mbias_ignore,nthreads,my
logobject.info('Methylation extraction complete')
return

def filt_POM(INfile,bedpath,mextDir,Rpath,pipev,my_session,logobject,blackListF=None):
def filt_POM(INfile,bedpath,mextDir,Rpath,Rlib,pipev,my_session,logobject,blackListF=None):
read_root=re.sub('_CpG.bedGraph','',os.path.basename(INfile))
Rfilt_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile
Rfilt_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile + ' ' + Rlib
if blackListF is None:
mv_cmd='mv -v '+ re.sub('_CpG.bedGraph','.CpG.filt.bed',INfile) + ' ' + re.sub('_CpG.bedGraph','.CpG.filt2.bed',INfile) + ';sleep 300'
cmd_all=';'.join([Rfilt_cmd,mv_cmd])
else:
SNP_filt=os.path.join(bedpath,'bedtools') + ' intersect -v -a' + re.sub('_CpG.bedGraph','.CpG.filt.bed',INfile) + ' -b ' + blackListF + ' > ' + re.sub('_CpG.bedGraph','.CpG.filt2.bed',INfile) + ';sleep 300'
SNP_filt=bedpath +' bedtools' + ' intersect -v -a' + re.sub('_CpG.bedGraph','.CpG.filt.bed',INfile) + ' -b ' + blackListF + ' > ' + re.sub('_CpG.bedGraph','.CpG.filt2.bed',INfile) + ';sleep 300'
cmd_all=';'.join([Rfilt_cmd,SNP_filt])
logobject.info(cmd_all)
with open(os.path.join(mextDir,"logs","%s.MetDack_filt.out" % read_root),'w') as stdoutF, open(os.path.join(mextDir,"logs","%s.MetDack_filt.err" % read_root),'w') as stderrF:
Expand Down
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8 changes: 4 additions & 4 deletions BSmethXT_WGBS.py~
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Expand Up @@ -68,7 +68,7 @@ def methXT_POM(INfile,QCdir,OUTpfx,refG,POMpath,mextDir,mbias_ignore,nthreads,my
drmaa_session = my_session,
run_locally = False,
working_directory = os.getcwd(),
job_other_options = '-p bioinfo --nodes 1=1 --mincpus='+str(nthreads))
job_other_options = '-p bioinfo --nodes=1=1 --mincpus='+str(nthreads))
stdoutF.write("".join(stdout_res))
stderrF.write("".join(stderr_res))

Expand All @@ -80,14 +80,14 @@ def methXT_POM(INfile,QCdir,OUTpfx,refG,POMpath,mextDir,mbias_ignore,nthreads,my
logobject.info('Methylation extraction complete')
return

def filt_POM(INfile,bedpath,mextDir,Rpath,pipev,my_session,logobject,blackListF=None):
def filt_POM(INfile,bedpath,mextDir,Rpath,Rlib,pipev,my_session,logobject,blackListF=None):
read_root=re.sub('_CpG.bedGraph','',os.path.basename(INfile))
Rfilt_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile
Rfilt_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile + ' ' + str(Rlib)
if blackListF is None:
mv_cmd='mv -v '+ re.sub('_CpG.bedGraph','.CpG.filt.bed',INfile) + ' ' + re.sub('_CpG.bedGraph','.CpG.filt2.bed',INfile) + ';sleep 300'
cmd_all=';'.join([Rfilt_cmd,mv_cmd])
else:
SNP_filt=os.path.join(bedpath,'bedtools') + ' intersect -v -a' + re.sub('_CpG.bedGraph','.CpG.filt.bed',INfile) + ' -b ' + blackListF + ' > ' + re.sub('_CpG.bedGraph','.CpG.filt2.bed',INfile) + ';sleep 300'
SNP_filt=bedpath +' bedtools' + ' intersect -v -a' + re.sub('_CpG.bedGraph','.CpG.filt.bed',INfile) + ' -b ' + blackListF + ' > ' + re.sub('_CpG.bedGraph','.CpG.filt2.bed',INfile) + ';sleep 300'
cmd_all=';'.join([Rfilt_cmd,SNP_filt])
logobject.info(cmd_all)
with open(os.path.join(mextDir,"logs","%s.MetDack_filt.out" % read_root),'w') as stdoutF, open(os.path.join(mextDir,"logs","%s.MetDack_filt.err" % read_root),'w') as stderrF:
Expand Down
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44 changes: 40 additions & 4 deletions BSstats_WGBS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@

#####DEFINITIONS#################################################

def single_CpG_limma(ii,sampleInfo,outdir,Rpath,pipev,my_session,logobject):
Rstat_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii +';sleep 300'
def single_CpG_limma(ii,sampleInfo,outdir,Rpath,Rlib,pipev,my_session,logobject):
Rstat_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii + ' ' + Rlib +' ;sleep 300'
logobject.info(Rstat_cmd)
with open(os.path.join(outdir,"logs","singleCpG_stats.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","singleCpG_stats.err"),'w') as stderrF:
try:
Expand All @@ -36,8 +36,44 @@ def single_CpG_limma(ii,sampleInfo,outdir,Rpath,pipev,my_session,logobject):
logobject.info('Single CpG stats calculation complete')
return

def int_stats_limma(ii,bedList,sampleSheet,outdir,Rpath,pipev,my_session,logobject):
cmd_all=[os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.interval_stats.limma.R ' + outdir + ' ' + li + ' ' + ii + ' ' + sampleSheet for li in bedList]
def mCT_get_CpGxInt(ii,outList,refG,bedList,outdir,bedpath,my_session,logobject):
os.chdir(outdir)
pozF=os.path.join(outdir,re.sub('.fa*','.poz',os.path.basename(refG)))
imdF=os.path.join(outdir,re.sub('.poz','.CpG.bed',os.path.basename(pozF)))
if not os.path.exists(imdF):
cmd0='grep "+" ' + pozF + ' | awk \'{print $1, $5, $5+1, $6, $8}\' - | tr " " "\\t" | sort -k 1,1 -k2,2n - > ' + imdF
cmd1=[bedpath +' bedtools' + ' intersect -wa -a ' + imdF + ' -b ' + bli + ' > ' + oli for bli,oli in zip(bedList,outList) ]
cmd_all=cmd1
cmd_all[0:0]=[cmd0]
cmd_all_str=';'.join(cmd_all)
else:
cmd1=[bedpath +' bedtools' + ' intersect -wa -a ' + imdF + ' -b ' + bli + ' > ' + oli for bli,oli in zip(bedList,outList) ]
cmd_all=cmd1
cmd_all_str=';'.join(cmd_all)
logobject.info(cmd_all_str)
with open(os.path.join(outdir,"logs","interval_CpG_prep.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","interval_CpG_prep.err"),'w') as stderrF:
try:
stdout_res, stderr_res = run_job(cmd_str = cmd_all_str,
job_name = 'int_prep',
logger = logobject,
drmaa_session = my_session,
run_locally = False,
working_directory = os.getcwd(),
job_other_options = '-p bioinfo')
stdoutF.write("".join(stdout_res))
stderrF.write("".join(stderr_res))

# relay all the stdout, stderr, drmaa output to diagnose failures
except Exception as err:
logobject.error("Interval CpG preparation error: %s" % err)
raise
else:
logobject.info('Interval CpG preparation complete')
return


def int_stats_limma(ii,bedList,auxList,sampleSheet,outdir,Rpath,Rlib,pipev,my_session,logobject):
cmd_all=[os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.interval_stats.limma.R ' + outdir + ' ' + li +' '+ aui +' ' + ii + ' ' + sampleSheet + ' ' + Rlib for li,aui in zip(bedList,auxList)]
cmd_all_str=';'.join(cmd_all)
logobject.info(cmd_all_str)
with open(os.path.join(outdir,"logs","interval_stats.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","interval_stats.err"),'w') as stderrF:
Expand Down
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44 changes: 40 additions & 4 deletions BSstats_WGBS.py~
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@ import collections as cll

#####DEFINITIONS#################################################

def single_CpG_limma(ii,sampleInfo,outdir,Rpath,pipev,my_session,logobject):
Rstat_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii +';sleep 300'
def single_CpG_limma(ii,sampleInfo,outdir,Rpath,Rlib,pipev,my_session,logobject):
Rstat_cmd=os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii + ' ' + Rlib +' ;sleep 300'
logobject.info(Rstat_cmd)
with open(os.path.join(outdir,"logs","singleCpG_stats.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","singleCpG_stats.err"),'w') as stderrF:
try:
Expand All @@ -36,8 +36,44 @@ def single_CpG_limma(ii,sampleInfo,outdir,Rpath,pipev,my_session,logobject):
logobject.info('Single CpG stats calculation complete')
return

def int_stats_limma(ii,bedList,sampleSheet,outdir,Rpath,my_session,logobject):
cmd_all=[os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v1.0.1/WGBSpipe.interval_stats.limma.R ' + outdir + ' ' + li + ' ' + ii + ' ' + sampleSheet for li in bedList]
def mCT_get_CpGxInt(ii,outList,refG,bedList,outdir,bedpath,my_session,logobject):
os.chdir(outdir)
pozF=os.path.join(outdir,re.sub('.fa*','.poz',os.path.basename(refG)))
imdF=os.path.join(outdir,re.sub('.poz','.CpG.bed',os.path.basename(pozF)))
if not os.path.exists(imdF):
cmd0='grep "+" ' + pozF + ' | awk \'{print $1, $5, $5+1, $6, $8}\' - | tr " " "\\t" | sort -k 1,1 -k2,2n - > ' + imdF
cmd1=[bedpath +' bedtools' + ' intersect -wa -a ' + imdF + ' -b ' + bli + ' > ' + oli for bli,oli in zip(bedList,outList) ]
cmd_all=cmd1
cmd_all[0:0]=[cmd0]
cmd_all_str=';'.join(cmd_all)
else:
cmd1=[os.path.join(bedpath,'bedtools') + ' intersect -wa -a ' + imdF + ' -b ' + bli + ' > ' + oli for bli,oli in zip(bedList,outList) ]
cmd_all=cmd1
cmd_all_str=';'.join(cmd_all)
logobject.info(cmd_all_str)
with open(os.path.join(outdir,"logs","interval_CpG_prep.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","interval_CpG_prep.err"),'w') as stderrF:
try:
stdout_res, stderr_res = run_job(cmd_str = cmd_all_str,
job_name = 'int_prep',
logger = logobject,
drmaa_session = my_session,
run_locally = False,
working_directory = os.getcwd(),
job_other_options = '-p bioinfo')
stdoutF.write("".join(stdout_res))
stderrF.write("".join(stderr_res))

# relay all the stdout, stderr, drmaa output to diagnose failures
except Exception as err:
logobject.error("Interval CpG preparation error: %s" % err)
raise
else:
logobject.info('Interval CpG preparation complete')
return


def int_stats_limma(ii,bedList,auxList,sampleSheet,outdir,Rpath,Rlib,pipev,my_session,logobject):
cmd_all=[os.path.join(Rpath,'Rscript') +' --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/' + pipev + '/WGBSpipe.interval_stats.limma.R ' + outdir + ' ' + li +' '+ aui +' ' + ii + ' ' + sampleSheet + ' ' + Rlib for li,aui in zip(bedList,auxList)]
cmd_all_str=';'.join(cmd_all)
logobject.info(cmd_all_str)
with open(os.path.join(outdir,"logs","interval_stats.out" ),'w') as stdoutF, open(os.path.join(outdir,"logs","interval_stats.err"),'w') as stderrF:
Expand Down
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