if [ -z "$ERANGEPATH" ]
then
- ERANGEPATH='../commoncode'
+ ERANGEPATH='../erange'
fi
-echo 'runRNAPairedAnalysis.sh: version 3.7'
+echo 'runRNAPairedAnalysis.sh: version 3.8'
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: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'
# 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
-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
-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
-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
-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
-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
-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
-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
-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
-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
-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