matrix_gen.sh

   1 #!/bin/sh
   2 # Taking a list of DNA files (on stdin) and a comparator script
   3 # and scratch directory name (as parameters), produce a DNA-DNA
   4 # matrix listing real-valued [0,1] distance between each two DNA
   5 # files (on stdout).
   6
   7 # The comparator script will get five parameters: two filenames
   8 # to compare, interspersed with respective numbers of the samples,
   9 # and a directory name it can use as a scratch area, for caching
  10 # data between invocations. It is expected to output a single [0,1]
  11 # real-valued number representing the distance (0 is same, 1 is
  12 # totally dissimilar).
  13
  14 cmp="$1"
  15 scratch="$2"
  16
  17 mkdir -p "$scratch"
  18 cat >"$scratch/files"
  19
  20 in=0
  21 while read i; do
  22         jn=0
  23         while read j; do
  24                 echo "$("$cmp" "$i" $in "$j" $jn "$scratch") $in $jn"
  25                 # echo "$in $jn ($cmp $i $in $j $jn $scratch)" >&2
  26                 jn=$((jn+1))
  27         done <"$scratch/files"
  28         in=$((in+1))
  29 done <"$scratch/files"