Assuming that your input file contains only FASTA header records and sequence records (i.e., no blank lines, comment lines, etc.), you might do something like (untested): 

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 $record = <$read_filehandle>) {

    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

    }

[download]
(I'm not sure about the codon codes I've used to define $rx_sequence; please double-check this. (Update: Note, also, that the sequence letters I've used are all upper-case, but IIRC these can also be lower-case.))

Give a man a fish:  <%-{-{-{-<

In reply to Re^7: How to write to a file? by AnomalousMonk
in thread How to count the length of a sequence of alphabets and number of occurence of a particular alphabet in the sequence? by davi54

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