erange version 4.0a dev release

[erange.git] / docs / runStrandedAnalysis.sh

diff --git a/docs/runStrandedAnalysis.sh b/docs/runStrandedAnalysis.sh
index 2626ed05ff47dc879869fbd0006c09b761ec692a..44459019f601732e67f652eed96becc38d0d920d 100755 (executable)
--- a/docs/runStrandedAnalysis.sh
+++ b/docs/runStrandedAnalysis.sh
@@ -11,10 +11,10 @@
 
 if [ -z "$ERANGEPATH" ]
 then
-    ERANGEPATH='../commoncode'
+    ERANGEPATH='../erange'
 fi
 
-echo 'runStrandedAnalysis.sh: version 4.1'
+echo 'runStrandedAnalysis.sh: version 4.2'
 
 if [ -z "$1" ]
 then
@@ -34,39 +34,39 @@ python $ERANGEPATH/recordLog.py rna.log runStrandedAnalysis.sh "with parameters:
 # count the unique reads falling on the gene models ; the nomatch files are 
 # mappable reads that fell outside of the Cistematic gene models and not the 
 # unmappable of Eland (i.e, the "NM" reads)
-python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count -stranded -markGID -cache 1
+python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count --stranded --markGID --cache 1
 
 # calculate a first-pass RPKM to re-weigh the unique reads,
 # using 'none' for the splice count
-python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.count none $2.firstpass.rpkm -cache
+python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.count none $2.firstpass.rpkm --cache
 
 # recount the unique reads with weights calculated during the first pass
-python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.firstpass.rpkm $2.uniqs.recount -stranded -uniq -cache 1
+python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.firstpass.rpkm $2.uniqs.recount --stranded --uniq --cache 1
 
 # count splice reads
-python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count -stranded -splices -noUniqs -cache 1
+python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count --stranded --splices --noUniqs --cache 1
 
 # find new regions outside of gene models with reads piled up 
-python $ERANGEPATH/findall.py RNAFARP $2.rds $2.newregions.txt -RNA -minimum 1 -nomulti -flag NM -strandfilter plus -log rna.log -cache 1
-python $ERANGEPATH/findall.py RNAFARM $2.rds $2.newregions.txt -RNA -minimum 1 -nomulti -flag NM -strandfilter minus -log rna.log -cache 1 -append
+python $ERANGEPATH/findall.py RNAFARP $2.rds $2.newregions.txt --RNA --minimum 1 --nomulti --flag NM --strandfilter plus --log rna.log --cache 1
+python $ERANGEPATH/findall.py RNAFARM $2.rds $2.newregions.txt --RNA --minimum 1 --nomulti --flag NM --strandfilter minus --log rna.log --cache 1 --append
 
 # filter out new regions that overlap repeats more than a certain fraction
-python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good -startField 1 -log rna.log -cache 1
+python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good --startField 1 --log rna.log --cache 1
 
 # Alternative 2: use a precomputed list of "new" regions (outside of gene models)
 #python $ERANGEPATH/regionCounts.py $3 $2.nomatch.bed $2.newregions.good $2.stillnomatch.bed
 #python $ERANGEPATH/regionCounts.py $3 $2.rds $2.newregions.good 
 
 # map all candidate regions that are within a given radius of a gene in bp
-python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt -radius $4 -trackfar -stranded -cache
+python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt --radius $4 --trackfar --stranded --cache
 
 # calculate expanded exonic read density
-python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.recount $2.splices.count $2.expanded.rpkm $2.candidates.txt $2.accepted.rpkm -cache
+python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.recount $2.splices.count $2.expanded.rpkm $2.candidates.txt $2.accepted.rpkm --cache
 
 # weigh multi-reads
-python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi.count -accept $2.accepted.rpkm -stranded -multi -cache 1
+python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi.count --accept $2.accepted.rpkm --stranded --multi --cache 1
 
 # calculate final exonic read density
-python $ERANGEPATH/normalizeFinalExonic.py $2.rds $2.expanded.rpkm $2.multi.count $2.final.rpkm -multifraction -withGID -cache
+python $ERANGEPATH/normalizeFinalExonic.py $2.rds $2.expanded.rpkm $2.multi.count $2.final.rpkm --multifraction --withGID --cache
 
 fi