Mercurial > repos > md-anderson-bioinformatics > heat_map_creation

comparison heatmap.sh @ 34:58437af2d675 draft

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author insilico-bob
date Thu, 08 Feb 2018 14:45:46 -0500
parents 0097750ad7ad
children 605ec840a06b
comparison
equal deleted inserted replaced
33:0097750ad7ad 34:58437af2d675
1 #echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} 1 #echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18}
2 2
3 #get tool data and tool install directories
4 tooldir=$(cut -d';' -f1 <<< ${12})
5 tooldata=$(cut -d';' -f2 <<< ${12})
6
3 #create temp directory for row and col order and dendro files. 7 #create temp directory for row and col order and dendro files.
4 tdir=${12}/$(date +%y%m%d%M%S) 8 tdir=$tooldata/$(date +%y%m%d%M%S)
5 echo $tdir 9 echo $tdir
6 mkdir $tdir 10 mkdir $tdir
7 11
8 #run R to cluster matrix 12 #run R to cluster matrix
9 output="$(R --slave --vanilla --file=${12}/CHM.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)" 13 output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)"
10 rc=$?; 14 rc=$?;
11 if [ $rc != 0 ] 15 if [ $rc != 0 ]
12 then 16 then
13 echo $output; 17 echo $output;
14 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] 18 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
45 count=$((count+1)) 49 count=$((count+1))
46 done 50 done
47 echo "classifications " $classifications 51 echo "classifications " $classifications
48 echo "${11} " ${11} 52 echo "${11} " ${11}
49 #call java program to generate NGCHM viewer files. 53 #call java program to generate NGCHM viewer files.
50 java -jar ${12}/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt ${11} $classifications 54 java -jar $tooldir/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt ${11} $classifications
51 #clean up tempdir 55 #clean up tempdir
52 rm -rf $tdir 56 rm -rf $tdir