X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=docs%2FrunStandardAnalysis.sh;h=aa5fe60588a30ceba6a65301db81b13ac4f6051f;hp=6d83297bf4f39964793ced9800e46a3eb7bbcbc0;hb=0d3e3112fd04c2e6b44a25cacef1d591658ad181;hpb=5e4ae21098dba3d1edcf11e7279da0d84c3422e4

diff --git a/docs/runStandardAnalysis.sh b/docs/runStandardAnalysis.sh
index 6d83297..aa5fe60 100755
--- a/docs/runStandardAnalysis.sh
+++ b/docs/runStandardAnalysis.sh
@@ -11,25 +11,25 @@
 
 if [ -z "$ERANGEPATH" ]
 then
-    ERANGEPATH='../commoncode'
+    ERANGEPATH='../erange'
 fi
 
-echo 'runStandardAnalysis.sh: version 4.2'
+echo 'runStandardAnalysis.sh: version 4.3'
 
 models=""
 if [ $# -eq 5 ]; then
-    models=" -models "$5
+    models=" --models "$5
 fi
 
 replacemodels=""
 if [ $# -eq 6 ]; then
-    replacemodels=" -models $5 -replacemodels "
+    replacemodels=" --models $5 --replacemodels "
 fi
 
 if [ -z "$1" ]
 then
     echo
-    echo 'usage:runStandardAnalysis.sh genome rdsprefix repeatmaskdb bpradius [modelfile] [-replacemodels]'
+    echo 'usage:runStandardAnalysis.sh genome rdsprefix repeatmaskdb bpradius [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'
@@ -44,48 +44,48 @@ python $ERANGEPATH/recordLog.py rna.log runStandardAnalysis.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)
-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
+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
 
 # calculate a first-pass RPKM to re-weigh the unique reads,
 # using 'none' for the splice count
-echo "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
+echo "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
-echo "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
+echo "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
-echo "python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count -splices -noUniqs -cache 1  $models $replacemodels"
-python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count -splices -noUniqs -cache 1  $models $replacemodels
+echo "python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count --splices --noUniqs --cache 1  $models $replacemodels"
+python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count --splices --noUniqs --cache 1  $models $replacemodels
 
 # Alternative 1: find new regions outside of gene models with reads piled up 
-echo "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
+echo "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
 
 # Alternative 1: filter out new regions that overlap repeats more than a certain fraction
-echo "python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good -startField 1 -cache 1"
-python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good -log rna.log -startField 1 -cache 1
+echo "python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good --log rna.log --startField 1 --cache 1"
+python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good --log rna.log --startField 1 --cache 1
 
 # map all candidate regions that are within a given radius of a gene in bp
-echo "python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt -radius $4 -trackfar -cache  $models $replacemodels"
-python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt -radius $4 -trackfar -cache  $models $replacemodels
+echo "python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt --radius $4 --trackfar --cache  $models $replacemodels"
+python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt --radius $4 --trackfar --cache  $models $replacemodels
 
 # make sure candidates.txt file exists
 echo "touch $2.candidates.txt"
 touch $2.candidates.txt
 
 # calculate expanded exonic read density
-echo "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
+echo "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
-echo "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
+echo "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
-echo "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
+echo "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
\ No newline at end of file