updated version number

katsikora · Feb 27, 2018 · 5bad4bc · 5bad4bc
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commit 5bad4bc
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Showing 7 changed files with 9 additions and 9 deletions.
diff --git a/BS_DMR_WGBS.py b/BS_DMR_WGBS.py
@@ -39,7 +39,7 @@ def DMR_metilene(ii,sampleInfo,outfile,nthreads,metipath,my_session,logobject):
 
 
 def clean_up_metilene(metilene_out,CpG_stats_out,sampleInfo,outdir,my_session,logobject):
-    cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out + ' ' + CpG_stats_out +' ' + sampleInfo
+    cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v1.0.0/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out + ' ' + CpG_stats_out +' ' + sampleInfo
     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:

diff --git a/BS_DMR_WGBS.py~ b/BS_DMR_WGBS.py~
@@ -39,7 +39,7 @@ def DMR_metilene(ii,sampleInfo,outfile,nthreads,metipath,my_session,logobject):
 
 
 def clean_up_metilene(metilene_out,CpG_stats_out,sampleInfo,outdir,my_session,logobject):
-    cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v0.02/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out + ' ' + CpG_stats_out +' ' + sampleInfo
+    cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.metilene_stats.limma.R ' + outdir + ' ' + metilene_out + ' ' + CpG_stats_out +' ' + sampleInfo
     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:

diff --git a/BSmethXT_WGBS.py b/BSmethXT_WGBS.py
@@ -82,7 +82,7 @@ def methXT_POM(INfile,QCdir,OUTpfx,refG,POMpath,mextDir,mbias_ignore,nthreads,my
 
 def filt_POM(INfile,bedpath,mextDir,my_session,logobject,blackListF=None):
     read_root=re.sub('_CpG.bedGraph','',os.path.basename(INfile))
-    Rfilt_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile 
+    Rfilt_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v1.0.0/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile 
     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])

diff --git a/BSmethXT_WGBS.py~ b/BSmethXT_WGBS.py~
@@ -82,7 +82,7 @@ def methXT_POM(INfile,QCdir,OUTpfx,refG,POMpath,mextDir,mbias_ignore,nthreads,my
 
 def filt_POM(INfile,bedpath,mextDir,my_session,logobject,blackListF=None):
     read_root=re.sub('_CpG.bedGraph','',os.path.basename(INfile))
-    Rfilt_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v0.02/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile 
+    Rfilt_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.POM.filt.R ' + mextDir + ' ' + INfile 
     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])

diff --git a/BSstats_WGBS.py b/BSstats_WGBS.py
@@ -14,7 +14,7 @@
 #####DEFINITIONS#################################################
 
 def single_CpG_limma(ii,sampleInfo,outdir,my_session,logobject):
-    Rstat_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii +';sleep 300'
+    Rstat_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v1.0.0/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii +';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:
@@ -37,7 +37,7 @@ def single_CpG_limma(ii,sampleInfo,outdir,my_session,logobject):
     return
 
 def int_stats_limma(ii,bedList,sampleSheet,outdir,my_session,logobject):
-    cmd_all=['/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.interval_stats.limma.R ' + outdir + ' ' + li + ' ' + ii + ' ' + sampleSheet for li in bedList]
+    cmd_all=['/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v1.0.0/WGBSpipe.interval_stats.limma.R ' + outdir + ' ' + li + ' ' + ii + ' ' + sampleSheet for li in bedList]
     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:

diff --git a/BSstats_WGBS.py~ b/BSstats_WGBS.py~
@@ -14,7 +14,7 @@ import collections as cll
 #####DEFINITIONS#################################################
 
 def single_CpG_limma(ii,sampleInfo,outdir,my_session,logobject):
-    Rstat_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii
+    Rstat_cmd='/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.singleCpGstats.limma.R ' + outdir + ' ' + sampleInfo + ' ' + ii +';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:
@@ -38,7 +38,7 @@ def single_CpG_limma(ii,sampleInfo,outdir,my_session,logobject):
 
 def int_stats_limma(ii,bedList,sampleSheet,outdir,my_session,logobject):
     cmd_all=['/package/R-3.3.1/bin/Rscript --no-save --no-restore /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBSpipe.interval_stats.limma.R ' + outdir + ' ' + li + ' ' + ii + ' ' + sampleSheet for li in bedList]
-    cmd_all_str=';'.join(cmd_all)+';sleep 300'
+    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:
         try:

diff --git a/WGBSpipe_example_wrapper.sh b/WGBSpipe_example_wrapper.sh
@@ -5,7 +5,7 @@ export PATH=$PATH:/package/bwa-0.7.4/bin
 export R_LIBS_USER=/data/manke/repository/scripts/DNA_methylation/Rlibs.3.3.1
 source /data/boehm/sikora/miniconda3/bin/activate NGSpy2.7
 
-python /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/v0.02/WGBS.pipe.ruffus.py --readIn /data/processing3/WGBS_pipe_test_IN/reads --ref GRCz10 --wdir /data/processing3/WGBS_pipe_example_OUT --trimReads  --fqcIn /data/processing3/WGBS_pipe_test_IN/in_fastqc --batchSize 24 --intList /data/processing3/WGBS_pipe_test_IN/danRer10.cpgIsland.ext.sorted.chr25.noCHR.bed --sampleInfo /data/processing3/WGBS_pipe_test_IN/example_sampleSheet.csv --DMRpg metilene 
+python /data/manke/repository/scripts/DNA_methylation/WGBS_pipe/dev/WGBS_pipe_lite.py --readIn /data/processing3/WGBS_pipe_test_IN/reads --ref GRCz10 --wdir /data/processing3/WGBS_pipe_lite_example_OUT --trimReads 'auto'  --fqcIn /data/processing3/WGBS_pipe_test_IN/in_fastqc --batchSize 24 --intList /data/processing3/WGBS_pipe_test_IN/danRer10.cpgIsland.ext.sorted.chr25.noCHR.bed --sampleInfo /data/processing3/WGBS_pipe_test_IN/example_sampleSheet.csv  
 
 
 source deactivate