there could potentially be overlap in the $2-$3 value ranges, that is why $4 or the gene id id used because the same $2-$3 values can not exist in two different genes. To be extra sure the combination of $4 and $1 can be used to ensure this, that will look at only the gene in $4 on the chromosome in $1. That might be better as it will be a unique lookup key used in the search.

yes, after the search key or lookup value in found in file2 all its associated lines will be adjacent, one on top of the other...

Code:

...... SDBH
...... SDBH
...... SDBH

into the output)
yes, this is true... though the combination of $1 and $4 in file1 may be better to ensure a unique match and values are found faster.

yes this is correct, the conflicts in the english requirements have to do with the nature of the human genome and that it is ever-changing and still full of unknowns. The test being performed or utilized also factors in to it and can add additional complexity/conflicts.

Thank you very much for all of your help .

awk

Code:

awk '
FNR==NR{
  a[$4];
  chr[$4]=$1;
  min[$4]=$2;
  max[$4]=$3;
  next
}
{
  split($4,array,"_");
  print $0,(array[1] in a) && ($2>=min[array[1]] && $2<=max[array[1] && $1=chr[array[1]])?"exon":"intron"
}
' file1 OFS="\t" file2 > output