When glaring at your script, I can see that

• you do not chomp the $proteinfilename after reading it from STDIN. The real file name probably does not contain a newline at the end.
• if the open is not successful, your program continues. Are you really interested in the results, if the file cannot be found? Use the idiom

  open my $FH, '<', $filename or die "Cannot open: $!";
  [download]

• next takes a label as a parameter. There are no labels in your code.
• you do not indent the code. Once you are advanced enough to use loops, please also learn to indent the code. Without indentation, your code becomes write-only, unreadable mess for humans.

Hi serafinososi,

...If the line starts with “>” (it is the first line of a FASTA file) the line is not considered...

What if the line that starts with ">" is more than one in the file what happens?

If I understand the OP's question, using the data provided, if I may suggest (adding to what others have said) using perl function split may do like so:

use warnings;
use strict;

my $protein;

while (<DATA>) {
    if (/^>/) {
        next;
    }
    else {
        $protein = join '', split;
    }
}

my $number_of_F = grep { /F/ } split //, $protein;

print "The aminoacid sequence: ", $protein, " contains ", $number_of_F
+,
  " Phenylalanine aminoacids", $/;

__DATA__
>gi|403369491|gb|EJY84591.1| Transcriptional regulator, Sir2 family pr
+otein Oxytricha trifallax

MMKQLIKHNKNTPLFNFLRVKFSSTAATIQTQQTVNKPIESKFKEEKLDNYHDIYEKSKRLAEQISQSKS
+ FICFTGAGLSTSTGIPDYRSTSNTLAQTGAGAYELEISEEDKKSKTRQIRSQVQRAKPSISHMALHAL
+ME NGYLKHLISQNTDGLHLKSGIPYQNLTELHGNTTVEYCKSCSKIYFRDFRCRSSEDPYHHLTGRQC
+EDLK CGGELADEIVHFGESIPKDKLVEALTAASQSDLCLTMGTSLRVKPANQIPIQTIKNKGQLAIVN
+LQYTPF DEIAQIRMHSFTDQVLEIVCQELNIKIPEYQMKRRIHIIRNAETNEIVVYGSYGNHKNIKLS
+FMQRMEYI DNKNHVYLALDKEPFHIIPDYFNFQNINTDQEEVEFRIHFYGHNSEPYFQLTLPRQSILE
+LQAGEHLICD ITFDYDKLEWK
[download]

Deliberately incomplete, after all this is (your) homework, but you have some of your problems solved here... only because Oxytricha is a cute green thing

#!/usr/bin/perl -w 
use strict;

my @protein = ();
my $phenylcounter = 0;

open (my $PROTEFILE, '<', $ARGV[0])
   or die $!; # If the file is not existing it gives an error message 
     # yup, I avoid the <STDIN> idea, solved by you. 
      while ($line = <$PROTEFILE>) { # We read the lines of the file
                 next if $line =~ m/^>/; # If the line starts with ">"
+ is not considered.
         $line =~ s/\s//g; # all white spaces removed from the line
 # Using the translate command, the program counts the number of F in 
+the sequence, assigning it to a variable.
# left for you... tr/F//...
                 $phenylcounter++}
      }  # the while loop terminates
close $PROTEFILE; # and the program continues closing the file.

print "The aminoacid sequence", $ARGV[0], " contains ", $phenylcounter
+, " Phenylalanine aminoacids";
print "\n"; # followed by new line
 
[download]

Updated: ($phenilcounter != $phenylcounter), fixed now

You've been given excellent suggestions (!):

• choroba shows the three-argument open, including using lexically-scoped variables (don't use global variables for file opens).
• 2teez shows a crucial first step: always use strict; use warnings;
• pvaldes imparted a hint on counting the number of "F"s in the sequence

Not to confuse matters here, but for your future reference (since you appear to be on a bioinformatics path), consider becoming well acquainted with Bio::SeqIO and its set of related modules.

Just as there are well-developed modules to parse HTML, XML, and CSV files, Bio::SeqIO lives to do the same for Fasta and other such formats.

For example, to retrieve and process each sequence within a Fasta file, you can do the following:

use strict;
use warnings;
use Bio::SeqIO;

print "Please type the file name of the protein sequence data: ";
chomp( my $proteinfilename = <STDIN> );
print "\n";

my $fastaIN = Bio::SeqIO->new( -file => $proteinfilename, -format => '
+Fasta' );

while ( my $seq = $fastaIN->next_seq() ) {
    print $seq->seq, "\n";
}
[download]

Each sequence in the Fasta file is accessible using the $seq->seq notation. The first part before the arrow operator is the sequence object; the part after the arrow operator is the method. These methods are covered in detail in the Bio::Seq module's documentation. In the example above, the sequence is printed, but a character count could be done there, too.

Hope this helps!

Please don't remove the original text of a comment.

But if he keeps it, then teacher will know he cheated

hi! I have the same problem and i'm going crazy. HELP ME! My perl program is: #!/usr/bin/perl -w print "Please type the file name of the protein sequence data: "; $proteinfilename = <STDIN>; chomp $proteinfilename; unless ( open (PROTEINFILE, $proteinfilename) ) { print "File \"$proteinfilename\" doesn\'t seem to exist!!\n"; } $protein = <PROTEINFILE> ; $empty = " " , (<PROTEINFILE>); while ( $protein = <PROTEINFILE> ) { if ( $protein =~ /^>/ ) { next $protein; } else { $protein =~ s/\s//g ; $union = join ($empty, $protein); } }; close PROTEINFILE ; $quantif = $union; $count = ($quantif =~ tr/F//); print "The aminoacid sequence:\n$union\ncontains $count Tryptophan aminoacids\n\n"; the problem is the count!!!! thank you Alessandra