I would suggest developing a separate program to clean up your data and leave the working program alone. It's always preferable to have 'clean data' to process and 2 steps I think are easier to debug. For example

#!/usr/bin/perl
# cleanup.pl
use strict;
use warnings;

print 'PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename 
  or die "Cannot open '$prot_filename' because: $!";

my $out_filename = 'cleaned_'.$prot_filename;  
open my $OUTFILE, '>', $out_filename 
  or die "Cannot open '$out_filename' because: $!";
  
$/ = ''; # Set paragraph mode

my %fasta_seen;  # sequences seen so far
my $header;
my $count_in;
my $count_out;
while ( my $record = <$PROTFILE> ) {
  ++$count_in; 
  if ( $record =~ s/^>(.*)//m ){
    $header = $1;
    # skip fragments
    next if $header =~ /\(Fragments\)/i;
  };  
    
  # Remove comment line(s)
  $record =~ s/^\s*#.*//mg; 

  # trim trailing spaces  
  $record =~ s/\s+$//;

  # skip duplicated
  if ( $fasta_seen{ $record }++ ){
    print $OUTFILE "\n";
  } else {
    print $OUTFILE $header.$record."\n\n";
    ++$count_out;
  }
}
close $OUTFILE;
close $PROTFILE;
printf "%d records read from %s\n",$count_in,$prot_filename;
printf "%d records written to %s\n",$count_out,$out_filename;
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I'm sure acknowledge of perlmonks.org would be appreciated by the community here.

Thank you so much Poj. Will do.
:)

Hi, can someone tell me what's the mistake I'm doing in the following code? To be precise, in line- 'printf "%d duplicate records written\n",$name,$para,$out_filename;'?
I get an error:


Argument "sdAb_1193_LgLlama" isn't numeric in printf at ../duplicate.p
+l line 35, <$PROTFILE> chunk 165.
'Redundant argument in printf at ../duplicate.pl line 35, <$PROTFILE> 
+chunk 1164.'
[download]

#!/usr/bin/perl
# cleanup.pl
use strict;
use warnings;

print 'Enter protein sequence filename: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename
  or die "Cannot open '$prot_filename' because: $!";

my $out_filename = 'duplicates_entries_in_'.$prot_filename;
open my $OUTFILE, '>', $out_filename
  or die "Cannot open '$out_filename' because: $!";

$/ = ''; # Set paragraph mode

my $name;
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;

  # Trim trailing white space
  $para =~ s/\s+$//;

 # next FASTA_RECORD if $fasta_seen{ $para }++;
if ( $fasta_seen{ $para }++ ){
  printf "%d duplicate records written\n",$name,$para,$out_filename;
  next FASTA_RECORD;
}
}
print "\n";
[download]

2019-04-07 Athanasius added code tags and removed break tags within code