gistfile1.txt

#!/usr/bin/env perl

use strict;
use warnings;
use Bio::SeqIO;
no warnings 'uninitialized';

my $in  = Bio::SeqIO->new(-file => $ARGV[0] , '-format' => 'Fasta');
my $first_size = 0;
my $counter  = 0;
my $error_found =0;
while ( my $seq = $in->next_seq() ) {
  my $cur_size = $seq->length();
  if($counter ==0)
  {
    $first_size = $cur_size;
  }

  if($first_size == $cur_size)
  {
  }
  else
  {
    $error_found++;
    print "Error in sequence ".$seq->display_id().". Size is ".$cur_size." but expected ".$first_size."\n";
  }

  $counter++;
}

if( $error_found > 0)
{
  print "Sequences with errors: ".$error_found."\n";
}

print "Bases in each alignment: $first_size\n";
print "Number of sequences: ".$counter."\n";