3 # This is no longer supported. It is recommended that the pythin script of the same name be used instead.
5 # runStandardAnalysis.sh
8 # example: . $ERANGEPATH/runStandardAnalysis.sh mouse c2c12rna ../mm9repeats/rmask.db 20000
10 # assuming that we have rds database with the prefix c2c12rna.24R and that an RNAFAR analysis has already been run.
12 # set ERANGEPATH to the absolute or relative path to ERANGE, if it's not in the environment
14 if [ -z "$ERANGEPATH" ]
16 ERANGEPATH='../erange'
19 echo 'runStandardAnalysis.sh: version 4.3'
28 replacemodels=" --models $5 --replacemodels "
34 echo 'usage:runStandardAnalysis.sh genome rdsprefix repeatmaskdb bpradius [modelfile] [--replacemodels]'
36 echo 'where rdsprefix is the name of the rds file without the .rds extension'
37 echo 'use "none" for the repeatmaskdb if you do not have one'
42 arguments=$1' '$2' '$3' '$4' '$models' '$6
43 echo 'running with settings: ' $arguments
44 python $ERANGEPATH/recordLog.py rna.log runStandardAnalysis.sh "with parameters: $arguments"
46 # count the unique reads falling on the gene models ; the nomatch files are
47 # mappable reads that fell outside of the Cistematic gene models and not the
48 # unmappable of Eland (i.e, the "NM" reads)
49 echo "python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count --markGID --cache 1 $models $replacemodels"
50 python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.uniqs.count --markGID --cache 1 $models $replacemodels
52 # calculate a first-pass RPKM to re-weigh the unique reads,
53 # using 'none' for the splice count
54 echo "python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.count none $2.firstpass.rpkm --cache $models $replacemodels"
55 python $ERANGEPATH/normalizeExpandedExonic.py $1 $2.rds $2.uniqs.count none $2.firstpass.rpkm --cache $models $replacemodels
57 # recount the unique reads with weights calculated during the first pass
58 echo "python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.firstpass.rpkm $2.uniqs.recount --uniq --cache 1 $models $replacemodels"
59 python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.firstpass.rpkm $2.uniqs.recount --uniq --cache 1 $models $replacemodels
62 echo "python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count --splices --noUniqs --cache 1 $models $replacemodels"
63 python $ERANGEPATH/geneMrnaCounts.py $1 $2.rds $2.splices.count --splices --noUniqs --cache 1 $models $replacemodels
65 # Alternative 1: find new regions outside of gene models with reads piled up
66 echo "python $ERANGEPATH/findall.py RNAFAR $2.rds $2.newregions.txt --RNA --minimum 1 --nomulti --flag NM --log rna.log --cache 1"
67 python $ERANGEPATH/findall.py RNAFAR $2.rds $2.newregions.txt --RNA --minimum 1 --nomulti --flag NM --log rna.log --cache 1
69 # Alternative 1: filter out new regions that overlap repeats more than a certain fraction
70 echo "python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good --log rna.log --startField 1 --cache 1"
71 python $ERANGEPATH/checkrmask.py $3 $2.newregions.txt $2.newregions.repstatus $2.newregions.good --log rna.log --startField 1 --cache 1
73 # map all candidate regions that are within a given radius of a gene in bp
74 echo "python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt --radius $4 --trackfar --cache $models $replacemodels"
75 python $ERANGEPATH/getallgenes.py $1 $2.newregions.good $2.candidates.txt --radius $4 --trackfar --cache $models $replacemodels
77 # make sure candidates.txt file exists
78 echo "touch $2.candidates.txt"
79 touch $2.candidates.txt
81 # calculate expanded exonic read density
82 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"
83 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
86 echo "python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi.count --accept $2.accepted.rpkm --multi --cache 1 $models $replacemodels"
87 python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi.count --accept $2.accepted.rpkm --multi --cache 1 $models $replacemodels
89 # calculate final exonic read density
90 echo "python $ERANGEPATH/normalizeFinalExonic.py $2.rds $2.expanded.rpkm $2.multi.count $2.final.rpkm --multifraction --withGID --cache"
91 python $ERANGEPATH/normalizeFinalExonic.py $2.rds $2.expanded.rpkm $2.multi.count $2.final.rpkm --multifraction --withGID --cache