erange version 4.0a dev release

[erange.git] / docs / runRNAPairedAnalysis.sh

diff --git a/docs/runRNAPairedAnalysis.sh b/docs/runRNAPairedAnalysis.sh
index baf7f04664aa669a0c92211ad410f4bc79172dad..cf75b6a5c9047ebb94332f26e8af234b68f3e382 100755 (executable)
--- a/docs/runRNAPairedAnalysis.sh
+++ b/docs/runRNAPairedAnalysis.sh
@@ -11,25 +11,25 @@
 
 if [ -z "$ERANGEPATH" ]
 then
 
 if [ -z "$ERANGEPATH" ]
 then

-    ERANGEPATH='../commoncode'
+    ERANGEPATH='../erange'

 fi
 
 fi
 

-echo 'runRNAPairedAnalysis.sh: version 3.7'
+echo 'runRNAPairedAnalysis.sh: version 3.8'

 
 models=""
 if [ $# -eq 5 ]; then
 
 models=""
 if [ $# -eq 5 ]; then

-    models=" -models "$5
+    models=" --models "$5

 fi
 
 replacemodels=""
 if [ $# -eq 6 ]; then
 fi
 
 replacemodels=""
 if [ $# -eq 6 ]; then

-    replacemodels=" -models $5 -replacemodels "
+    replacemodels=" --models $5 --replacemodels "

 fi
 
 if [ -z "$1" ]
 then
     echo
 fi
 
 if [ -z "$1" ]
 then
     echo

-    echo 'usage:runRNAPairedAnalysis.sh genome rdsprefix repeatmaskdb [modelfile] [-replacemodels]'
+    echo 'usage:runRNAPairedAnalysis.sh genome rdsprefix repeatmaskdb [modelfile] [--replacemodels]'

     echo
     echo 'where rdsprefix is the name of the rds file without the .rds extension'
     echo 'use "none" for the repeatmaskdb if you do not have one'
     echo
     echo 'where rdsprefix is the name of the rds file without the .rds extension'
     echo 'use "none" for the repeatmaskdb if you do not have one'


@@ -45,37 +45,37 @@ python $ERANGEPATH/recordLog.py rna.log runRNAPairedAnalysis.sh "with parameters
 # mappable reads that fell outside of the Cistematic gene models and not the 
 # unmappable of Eland (i.e, the "NM" reads)
 echo "python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count -markGID -cache 1 $models $replacemodels"
 # mappable reads that fell outside of the Cistematic gene models and not the 
 # unmappable of Eland (i.e, the "NM" reads)
 echo "python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count -markGID -cache 1 $models $replacemodels"

-python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count -markGID -cache 1 $models $replacemodels
+python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count --markGID --cache 1 $models $replacemodels

 
 # calculate a first-pass RPKM to re-weigh the unique reads,
 # using 'none' for the splice count
 
 # 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 $models $replacemodels
+python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.count none $2.firstpass.rpkm --cache $models $replacemodels

 
 # recount the unique reads with weights calculated during the first pass
 
 # recount the unique reads with weights calculated during the first pass

-python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.firstpass.rpkm $2.uniqs.recount -uniq -cache 1 $models $replacemodels
+python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.firstpass.rpkm $2.uniqs.recount --uniq --cache 1 $models $replacemodels

 
 # count splice reads
 
 # count splice reads

-python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count -splices -noUniqs -markGID -cache 1 $models $replacemodels
+python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count --splices --noUniqs --markGID --cache 1 $models $replacemodels

 
 # find new regions outside of gene models with reads piled up 
 
 # find new regions outside of gene models with reads piled up 

-python $ERANGEPATH/findall.py RNAFAR $2.rds $2.newregions.txt -RNA -minimum 1 -nomulti -flag NM -log rna.log -cache 1
+python $ERANGEPATH/findall.py RNAFAR $2.rds $2.newregions.txt --RNA --minimum 1 --nomulti --flag NM --log rna.log --cache 1

 
 # filter out new regions that overlap repeats more than a certain fraction
 
 # 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.checked -startField 1 -log rna.log -cache 1
+python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.checked --startField 1 --log rna.log --cache 1

 
 # calculate the read densities
 
 # calculate the read densities

-python $ERANGEPATH/regionCounts.py $2.newregions.checked $2.rds $2.newregions.good -markRDS -cache -log rna.log
+python $ERANGEPATH/regionCounts.py $2.newregions.checked $2.rds $2.newregions.good --markRDS --cache --log rna.log

 
 # map all candidate regions that have paired ends overlapping with known genes
 
 # map all candidate regions that have paired ends overlapping with known genes

-python $ERANGEPATH/rnafarPairs.py $1 $2.newregions.good $2.rds $2.candidates.txt -cache $models $replacemodels
+python $ERANGEPATH/rnafarPairs.py $1 $2.newregions.good $2.rds $2.candidates.txt --cache $models $replacemodels

 
 # calculate expanded exonic read density
 
 # 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 $models $replacemodels
+python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.recount $2.splices.count $2.expanded.rpkm $2.candidates.txt $2.accepted.rpkm --cache $models $replacemodels

 
 # weigh multi-reads
 
 # weigh multi-reads

-python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi.count -accept $2.accepted.rpkm -multi -cache 1 $models $replacemodels
+python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi.count --accept $2.accepted.rpkm --multi --cache 1 $models $replacemodels

 
 # calculate final exonic read density
 
 # 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
 
 fi