[Bioperl-l] SeqIO bug?

Ryan Golhar golharam at umdnj.edu
Fri Feb 11 14:31:01 EST 2005

I have a bunch of cDNA sequences that I'm trying to process.  The
sequences are in FASTA format, but they are all missing the FASTA header
ie that just contain the sequence.  As a test to make sure I'm reading
them in correctly, I doing the following:

        my $seq_in = Bio::SeqIO->new(-file => "<myseqfile",
-format => 'fasta');
        my $seq = $seq_in->next_seq();
        print $seq->length;

It prints out a number, but reads the first line as the FASTA header
even though its not there.  Wouldn't it make more sense to either print
out an error message about the missing FASTA header, or read in the file
as just the sequence regardless of specifying the FASTA format?

If I try to read the sequence in as "raw", the length is always printed
out as 70...


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