UNIX for Dummies Questions & Answers

grep "pattern" file

grep -A1 "pattern" file

#  awk '/match this/ { print;getline;print}' infile
match this pattern
and print next line

SK1.scplasm1

Code:

5057-5146
Ref:
AGAAATGCAACGCGAGAGCGCTATTTTACCAACGAAGAATCTGTGCTTCATTTTTGTAAAACAAAAATGCAACGCGAGAGCGCTAATTTT

Gen:
AGAAATGCAACGCGAGAGCGCTATTTTACCAACGAAGAATCTGTGCTTCATTTTTGTAAAACAAAAATGCAANNCGAGAGCGCTNNTTTT

SK1.scplasm1
2903-2922
Ref:
CCTTGAACTTGCATCTAAAC

Gen:
CCTTGAACTTGCATCTAAAC



I get result

Code:

5056 N's and then AGAAATGCAACGCGAGAGCGCTATTTTACCAACGAAGAATCTGTGCTTCATTTTTGTAAAACAAAAATGCAANNCGAGAGCGCTNNTTTT(which is Gen:5057-5146) and nothing else



However my expected output is

Code:

2092 N's (to fill gap from 1-2092) then CCTTGAACTTGCATCTAAAC(which is Gen:2903-2922) then 2135 N's to fill the gap from 2923-5056 then AGAAATGCAACGCGAGAGCGCTATTTTACCAACGAAGAATCTGTGCTTCATTTTTGTAAAACAAAAATGCAACGCGAGAGCGCTAATTTT (which is Gen:5057-5146)



 and so on with the rest of the file.
Can you help me figure out whats not working in the code or how it can be changed?
Cheers and thanks in advance:)
Good day!!

---------- Post updated at 08:14 AM ---------- Previous update was at 08:06 AM ----------

Correction 
However my expected output is
 Code:
  2902 N's (to fill gap from 1-2902) then CCTTGAACTTGCATCTAAAC(which is Gen:2903-2922) then 2135 N's to fill the gap from 2923-5056 then AGAAATGCAACGCGAGAGCGCTATTTTACCAACGAAGAATCTGTGCTTCATTTTTGTAAAACAAAAATGCAACGCGAGAGCGCTAATTTT (which is Gen:5057-5146)

#!/usr/bin/perl
open I, "$ARGV[0]";
local $/;
$_=<I>;
while (/(.*)\n(\d+)-(\d+)\nRef:\n.*\n\nGen:\n(.*)/g){
  $h{$1}{"$2-$3"}=$4;
}
for $i (keys %h){
  @arr=sort {(split /-/,$a)[0]<=>(split /-/,$b)[0]} (keys %{$h{$i}});
  $x=1;
  for $j (@arr){
    $j=~/(\d+)-(\d+)/;
    $s{$i}.="N" x ($1-$x) . $h{$i}{$j};
    $x=$2+1;
  }
}
for $i (keys %s){
  print "$i\n";
  print "$s{$i}\n";
}