#!/usr/bin/perl
use strict;
use warnings;

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

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

my $report_name = $prot_filename.'_alanine_report';
open my $out_file, '>', $report_name
     or die "Cannot open '$report_name' because: $!";

my $rx_fasta_header = qr{ \A > }xms;  # header pattern - very naive
my $rx_sequence     = qr{ \A [ACDEFGHIKLMNPQRSTVWY_]+ \z }xms;  # plea
+se check

my $sequence;  # sequence accumulator - initially undefined

RECORD:
while (my $record = <$PROTFILE>) {

    chomp $record;  # get rid of newline, if any

    # fasta header - process any sequence accumulated so far
    if ($record =~ $rx_fasta_header) {
        
        # do not process if no sequence accumulated so far (i.e., firs
+t header)
        next RECORD if not defined $sequence;
        
        my $seq_len = length $sequence;
        my $seq_n_A = $sequence =~ tr/A//;;
        do_something_with($sequence, $seq_len, $seq_n_A);
        
        undef $sequence;  # prepare to process next sequence
        next RECORD;
        
        }

    # part of sequence - accumulate
    if ($record =~ $rx_sequence) {
        $sequence .= $record;  # accumulate sub-sequences (records)
        next RECORD;
        }

    die "bad record: '$record'";  # don't know what this is

    }

# show all results
print $out_file;
close $out_file;
[download]

Your input file seems to contain an empty line, but the script does not provide for it.

If empty lines are ok, you could define something like

my $rx_empty     = qr{ \A \s* \z }xms;  # empty line (or whitespace on
+ly)
[download]

and after the chomp

if ($record =~ $rx_empty) {
        # ignore
        next RECORD
}
[download]

All my coding suggestions are untested.

... the error: bad record: '' at ../alanine_vs_sequence_length_2.pl line 46, <$PROTFILE> line 42.

(soonix has already addressed this.)

... the outfile is empty.

Almost all processing of a sequence is done in the  do_something_with() subroutine, which you do not show. I assume this subroutine exists in your code because the code would not compile if it did not (because you're enabling strictures with strict). Because I cannot see the code, I cannot say why it produces no output.

Here's another version of your posted code, including do_something_with(). It's not complete because I still don't know exactly what you want to do with each sequence. I've also done some re-organization, and handled the case of a sequence resulting from a final FASTA record (which I had not considered before). I'm using autodie to simplify file I/O error reporting. Again, this is untested.

Read more... (2 kB)

---

Give a man a fish:  <%-{-{-{-<

I'm sorry I did not include my subroutines in the previous message. But, I am counting the length of the sequence in the subroutine but it's not working yet. I tried your suggestion as follows:

#!/usr/bin/perl
use strict;
use warnings;
use autodie;

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

open my $PROTFILE, '<', $prot_filename;

my $report_name = "${prot_filename}_alanine_report";
open my $out_file, '>', $report_name;

my $rx_fasta_header = qr{ \A > }xms;  # header pattern - very naive
my $rx_sequence     = qr{ \A [ACDEFGHIKLMNPQRSTVWY_]+ \z }xms;  # plea
+se check
my $rx_blank_line   = qr{ \A \s* \z }xms;

my $sequence;  # sequence accumulator - initially undefined

RECORD:
while (my $record = <$PROTFILE>) {

    # handle any records to be ignored here
    next RECORD if $record =~ $rx_blank_line;

    chomp $record;  # get rid of newline, if any

    # fasta header - process any sequence accumulated so far
    if ($record =~ $rx_fasta_header) {
       
        # do not process if no sequence accumulated so far (i.e., firs
+t header)
        next RECORD if not defined $sequence;
       
        do_something_with($sequence, $out_file);
       
        undef $sequence;  # prepare to process next sequence
        next RECORD;
       
        }

    # part of sequence - accumulate
    if ($record =~ $rx_sequence) {
        $sequence .= $record;  # accumulate sub-sequences (records)
        next RECORD;
        }

    die "bad record: '$record'";  # don't know what this is

    }  # end while RECORD loop

# handle any sequence accumulated from final FASTA record
do_something_with($sequence, $out_file) if defined $sequence;

# clean up
close $PROTFILE;
close $out_file;

exit;

# subroutines #

sub do_something_with {

    my ($sequence,  # accumulated sequence
        $fh,        # output filehandle
        ) = @_;

    my $seq_len = length $sequence;
    }
[download]

But I'm getting the error - bad record: 'SRALGMLAVDNQARVUHGPTVASLAPTFGRGAMTNHWVDIKNANLVVVMGGNAAEAHPVG' at ../alanine_vs_sequence_length_3.pl line 47, <$_...> line 1370. And I get this error for both your and my script. Does it have something to do with the "die" command on line 47 as it is pointing out?