UNIX for Dummies Questions & Answers

>S8_SK1.chr01
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTT
TGTATACTGATTTTACGTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

>S8_SK1.chr01
1-119       119   N=119
120-220     101   A=33 C=31 G=12 T=25
221-300     80    N=80

perl -F// -lane 'BEGIN{$a=1}if ($. > 1){$l=length;for $i (@F){$a{$i}++};printf "$a-" . ($l+$a-1) . "\t$l\t"; for $i (keys %h){printf "$i=$h{$i} "};printf "\n";%h=();$a+=$l}' file

1-100    100    
101-200    100    
201-300    100

perl -F// -lane 'BEGIN{$a=1}if ($. > 1){$l=length;for $i (@F){$h{$i}++};printf "$a-" . ($l+$a-1) . "\t$l\t"; for $i (keys %h){printf "$i=$h{$i} "};printf "\n";%h=();$a+=$l}' file

1-100    100    N=100 
101-200    100    A=28 T=16 C=28 N=19 G=9 
201-300    100    A=5 T=9 N=80 C=3 G=3

#!/usr/bin/perl
open I, "$ARGV[0]";
local $/;
$_=<I>;
s/^>.*\n//;
s/\n//g;
$a=1;
while (/N+|[ACGT]+/g){
  $s=$&;
  $l=length $s;
  @F=split //, $s;
  for $i (@F){
    $h{$i}++
  }
  print "$a-" . ($a+$l-1) . "\t$l\t";
  for $i (keys %h){
    print "$i=$h{$i} ";
  }
  print "\n";
  %h=();
  $a+=$l;
}

$1=~/(^>.*)/;
s/^>.*\n//;