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

[Fields, Christopher J]

I think you mean:

   my $in = Bio::SeqIO->new(-file => 'yourfile', -format => 'Fasta');
   my $seq = $in->next_seq;

chris

On Oct 12, 2013, at 9:56 PM, Jing Yu <logust79 at googlemail.com> wrote:

> Hi,
> 
> 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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>> Bioperl-l at lists.open-bio.org
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> 
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