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'
# 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)
# 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
# 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
-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
-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
-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
-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
-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
# 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
-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
-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