Shell Programming and Scripting

chr2L    22975381    -1.6723247    chr2L    22975381    -1.8917731    0.219448    0
chr2L    22975421    -1.526086    chr2L    22975421    -1.8669024    0.340816    0    
chr2L    22975458    -1.7168827    chr2L    22975458    -1.9361134    0.219231    0

2L    gadfly    exon    15748693    15748925    .    -    
2L    gadfly    exon    15748515    15748637    .    -    
2L    gadfly    exon    15746596    15748455    .    -

#!/bin/bash
> combined.txt
old_IFS=$IFS
IFS=$'\n'
for i in $(cat file1);do
    result=""
    for j in $(cat file2);do
        if [[ `echo $i |awk '{print $2}'` -gt `echo $j |awk '{print $4}'` && `echo $i |awk '{print $2}'` -lt `echo $j |awk '{print $5}'` ]];then
            result+="`echo $j|awk '{print $2}'`,"
        fi
    done
    result=`echo $result|sed 's/.$//'`
    echo $i $result >> combined.txt
done
IFS=$old_IFS

nawk '
  FNR==NR{f2s[FNR]=$4; f2f[FNR]=$5; f2[$4,$5]=$0;next}
  {
     for(i=1;i in f2s;i++)
       if ($2>=f2s[i] && $2<=f2f[i])
          print $0, f2[f2s[i], f2f[i]]
  }' file2 file1