Mercurial > repos > md-anderson-bioinformatics > heat_map_creation

comparison heatmap.sh @ 32:16593e40c2cd draft

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Version 2.0.5
author insilico-bob
date Thu, 20 Jul 2017 15:31:06 -0400
parents e2b3920e20c1
children 0097750ad7ad
comparison
equal deleted inserted replaced
31:e01b833f5d43 32:16593e40c2cd
1 echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} 1 echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17}
2
3 #run python to validate the input matrix and covariate files (if any)
4 #output="$(python ${11}/mda_heatmap_gen.py $@)"
5 output=$(python ${11}/mda_heatmap_gen.py "$@")
6 rc=$?;
7 echo $output;
8 if [ $rc != 0 ]
9 then
10 exit $rc;
11 fi
12
13
2 #create temp directory for row and col order and dendro files. 14 #create temp directory for row and col order and dendro files.
3 tdir=${11}/$(date +%y%m%d%M%S) 15 tdir=${11}/$(date +%y%m%d%M%S)
4 echo $tdir 16 echo $tdir
5 mkdir $tdir 17 mkdir $tdir
18
6 #run R to cluster matrix 19 #run R to cluster matrix
7 output="$(R --slave --vanilla --file=${11}/CHM.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${12} ${13} ${14} ${15} 2>&1)" 20 output="$(R --slave --vanilla --file=${11}/CHM.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${12} ${13} ${14} ${15} 2>&1)"
8 rc=$?; 21 rc=$?;
9 if [ $rc != 0 ] 22 if [ $rc != 0 ]
10 then 23 then