Try

my %fasta_seen;

FASTA_RECORD:
while ( my $para = <$PROTFILE> ) {
  # Remove fasta header line
  if ( $para =~ s/^>(.*)//m ){
     $name = $1;
  };
  # Remove comment line(s)
  $para =~ s/^\s*#.*//mg;

  next FASTA_RECORD if $fasta_seen{ $para }++;

  …

[download]

This may not be a sensible solution if your sequences are very long in which case consider using a message digest like Digest::MD5

poj

In reply to Re^11: how to read input from a file, one section at a time? by poj
in thread how to read input from a file, one section at a time? by davi54

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