[Bioperl-l] How does '-alphabet' help? Is there any function which could remove "wrong" characters?

Jing Yu logust79 at googlemail.com
Sun Oct 13 02:56:40 UTC 2013


my $text = <INFILE>; only reads a line. 

Why not just do:

my $seq1 = Bio::Seq->new(-file => 'yourfile', -format => 'Fasta');

On 13 Oct 2013, at 10:48, Vasily Aushev <vaushev at gmail.com> wrote:

> in my very simple script, I am reading the sequence from the file by
> my $text = <INFILE>;
> and then making a new sequence object:
> my $seq1 = Bio::Seq->new(-seq => $text, -alphabet => 'dna' );
> After spending some time, I found that the 'carriage return' character
> (0x0D) which occurs at the end of my string (it's a Windows file) causes
> problems (exceptions) on further processing. I thought that defining the
> -alphabet for the sequence object should remove this "wrong" character, but
> it's not the case. So, my question - is there any function for removing all
> characters which are not part of defined alphabet?
> Thanks in advance!
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