#!/bin/bash

# Run this from day.1/data

DATA=.
SCRIPTS=../../scripts

# Change this to the directory where Circos is installed 
CIRCOS=/home/martink/work/circos/svn/

echo "Creating list of 16,000 genes"
cat conservation/coords.txt | awk '{print $2,$3,$4,$4-$3+1,"name="$1}' > genes.txt

BINS="5 10 20 50 100"

for ws in $BINS; do
  echo "Counting genes in $ws kb bins"
  bin=$((ws * 1000))
  cat genes.txt | ~/work/circos/svn/tools/resample/bin/resample -bin $bin -count > genes.count.${ws}kb.txt
done

for ws in $BINS; do
  bin=$((ws * 1000))
  echo "Counting genes in $ws kb bins"
  cat genes.txt | $CIRCOS/tools/resample/bin/resample -bin $bin -count > genes.count.${ws}kb.txt
  echo "Calculating gene average size in $ws kb bins"
  cat genes.txt | $CIRCOS/tools/resample/bin/resample -bin $bin -avg > genes.avgsize.${ws}kb.txt
done

for type in conservation duplication; do
  echo "Creating $type links"
  cat $type/C* $type/S* $type/Z* | $SCRIPTS/create.yeast.links -coord $type/coords.txt > links.$type.txt
  echo "...extracting largest 10,000 links"
  N=10000
  cat links.$type.txt | awk '{print $3-$2+1,$0}' | sort -nr | head -$N | cut -d " " -f 2- > links.$type.$N.txt

  for ws in $BINS; do
      bin=$((ws * 1000))
      echo "...counting links in $ws kb bins"
      cat links.$type.txt | $CIRCOS/tools/binlinks/bin/binlinks -bin $bin -num > links.$type.count.${ws}kb.txt
  done

done