It now appears that your data file was created on a windows system and you are reading it with a unix-like system. Perl can handle this, but you have to tell it using IO layers in the open statement. (Refer perlio) 
use strict;
use warnings;
BEGIN {
    my $win_file # memory file simulates windows file.
    = ">symbB.v1.2.017277.t1|scaffold1325.1|size176917|3\r\n"

    . "acggaccgcggcatttgccaatttgcgcgt"
    . "cgtcgggggtcgccatgatgtttcgcttgg"
    . "caggcttttttgctttggcactgctggtcg"
    . "cgggaaagcc\r\n"

    . "caagggtggcaaaggtgcaaaaggagaaca"
    . "agaccccttctctgagcttagccgcctcgc"
    . "agacaatttgaaagatgctaaagaacagcc"
    . "ggagaaggcc\r\n"

    . "aagaatgctctgaacatgatggatccagaa"
    . "agtttaggcgattctatggccaacatgatg"
    . "gtgatggcaatggataaggaccaggatggt"
    . "gtgttgtcag\r\n"
    ;
    $ARGV[0] = \do{$win_file};
}

open( my $input, '<:crlf', $ARGV[0] )
    or die( "Could not open input file $ARGV[0].\n" );

my $seq;
while ( my $line = <$input> ) {
    chomp($line);
    unless ( $line =~ m/>/ ) {
        $line = uc($line);
        $seq .= $line;
    }
}
print "Length of \$seq is ", length($seq), " characters\n";

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Bill

In reply to Re: missing character when reading input file by BillKSmith
in thread missing character when reading input file by JediGorf

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