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.

poj

In reply to Re^18: 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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