Dear monks, I am trying to learn perl and am starting by trying to parse files. Anyway, I simply want to count the number of characters in each gene in a file but am getting stuck. I wondered if someone may be able to help? The file looks like this: I want to count the sequence characters seperated by each >gb|..... line. Many thanks 

>gb|AE008689|:2073051-2073458, Atu4895
TTGGTCACATATTTTCGCTATTCGAAACCCAAATATCCCTGCGGAACACGTTTTATTGGAGCCGCCGTTT
TGCAGTTGCTCGGTGCTGGATTCTTGGCGTTCGTCTTTTGTCTGCTGGATGGGCTCACTGCAAAACCAAC
GATAATTCTCGGTCAGTTTGTATCATGCCTAGTGGGGAGCGTCGCCGGCTTTCATTTCGTGGCTTTTCGT
CGCCCAGGCACGGACGGCCAACTTTACCTTATCGCGACGTCGCTCTTGGCATTTGGGACCCATTATTGGC
TGGTGTCATATTCATTACCTGACCTTTTGCTAGCAAGATTGATTTCAGGATTTGGATCGGGTGTGGTTGT
TGCAGGAACTTTCCGACGTCGCTTTCTGGAAAATCCGGTAATTCCCTGCGTTCGATAG
>gb|AE008689|:c2074151-2073549, Atu4896
GTGTTTGGACCATATTTTCTGTGCAAACTAAACGATGACATAGGGCGATTTTTAGTGGCGGACAAATACA
GACTTCCCGAAGAGTTTTTTACCACTCGGTTTCTCGTTAGACGCATCGTACCCACAGACGCTGAAGCTAT
TTTCGAAGGGTGGAACACCGATCCCGAGGTGACGAAGTACCTGACGTGGAAACCCCACTCCGAGCTTGGC
CAGACACAGCGGGCGATTGAAGAAAATTATAGTGCGTGGAATGCAGGTACATCGTTTCCAGCTGTCATCT
GCCATCGCGAACGGCCACATGAACTAATCGGCCGTATTGATGCACGTCCGATGGGCCACAAGGTCTCTTA
CGGGTGGCTTGTCCGAAGAACCTGGTGGGGCCGGGGTGTTGCAAGCGAGGTCGTTCAACTCGCTGTAGAA
CACGCGTTATCGCATCCGCGCATCTTTCGCACCGAAGCATCCTGCGACGTTCTGAACACGGCGTCAGCAA
GAGTGATGGAAAAAGTAGGGATGACAAAGGAGGCCGTGCTTCGACGGTACCTTTTTCACCCCAATTTTTC
GAATATGCCGCGAGACGCCTTCCTGTATTCCAAGGTACGTTAA
>gb|AE008689|:c2074749-2074345, Atu4897
ATGAAACATACCATCGCAGTTCTCGGCCTGATCACCTTCTCCAGCCCGGCCTTCGCAGCATCGTGCGAGA
AAAACTTCACCGTCTCAGGCGTACCGATGGTCACGGCTGTCTCTTACAAATCCTTTCAGGAACTGCCGAA
AGCCAAAGCACCAGCTGTCCTTCAAAAGCTCGCCCAGGCCGTCGCGGCAGAAGGTTTTTCAGGTATCCAG
ATCAACAAGGCACTGTCGTCAATCGATGCCCATCAGGAAACCAGCGGAAGTGGCAGGATTCAGACGCTGC
GGGTTGTCGCCCGCCAGAAAGGCGCCGCTGTCCGGATCGATGCTGTCTTCAATATTCAGGCAGGACAGAT
CGCCGACAAAGACGTCATCCGCAAGGGCATCTGCGACATCATAAAAGGCGCGTAA

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and this is where i've got to with the code... 
#! /usr/bin/perl -w

use strict;

my $num_of_params;

$num_of_params = @ARGV;

if ($num_of_params < 2)    {
    die ("\nYou haven't entered enough parameters!\n\nTo run the progr
+am type:\n\t\tperl gc3s_content.pl infile.ffn outfile.gc3s \n\n\t\tWh
+ere window_size is the size of each window for which the program will
+ calculate results\n");
}

open (INFILE, $ARGV[0]) or die "unable to open file $!";
open (OUTFILE,">$ARGV[1]") or die "unable to open file $!";

my @fasta = <INFILE>;
my @gene;
my $gene;
my $flag;

foreach my $line (@fasta)  {

    if ($line =~ /^>/)   {
   #           print "$line\n";
       $flag = 0;
    }

  #  elsif ($line !~ /^>/) {
     elsif ($line =~ /^\w+/)  {

      $gene = $line;
      $flag = 1;

   }

   if ($flag)  {
     chomp ($gene);
     $gene .= $line;

   }


}


print "$gene\n";

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In reply to parsing question by Anonymous Monk

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