docs/buildMatrix.sh

   1 #!/bin/bash
   2 echo 'buildMatrix.sh: version 1.2'
   3
   4 indexPrev=0
   5 indexCur=0
   6
   7 truncateRPKM=""
   8 if [ $# -eq 3 ]; then
   9     truncateRPKM="--truncate "$3
  10 fi
  11
  12 if [ $# -eq 4 ]; then
  13     truncateRPKM="--rescale --truncate "$3
  14 fi
  15
  16 if [ $# -lt 2 ]; then
  17         echo 'usage: buildMatrix.sh name datalist.file [truncateRPKM] [--rescale]'
  18         echo
  19         echo 'where the datalist file is a comma-delimited list of prefix and rds-files'
  20         echo
  21 else
  22         python $ERANGEPATH/recordLog.py buildMatrix.log buildMatrix.sh "with parameters: $1 $2 $truncateRPKM"
  23         while read line
  24         do
  25                 prefix=`echo $line | cut -f 1 -d ','`
  26                 filename=$prefix.partcount
  27                 if [ -e $filename ]; then
  28                         if [ $indexCur -lt 1 ]; then
  29                                 echo "building $1.step0"
  30                                 echo -e '\t' > $1.step0
  31                                 cut -f 1 $filename >> $1.step0
  32                                 indexCur=1
  33                         fi
  34                                 python $ERANGEPATH/buildMatrix.py $1.step$indexPrev $filename $1.step$indexCur $truncateRPKM
  35                                 rm $1.step$indexPrev
  36                                 let indexPrev=indexPrev+1
  37                                 let indexCur=indexCur+1
  38                 else
  39                         echo "could not find $filename - skipping"
  40                         python $ERANGEPATH/recordLog.py buildMatrix.log buildMatrix.sh "could not find $rds - skipping"
  41                 fi
  42         done < $2
  43         mv $1.step$indexPrev $1.matrix.tab
  44 fi