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

[Jing Yu]

Oh, of course yes. Thanks for correction ;)

Jing
On 13 Oct 2013, at 11:38, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> 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!
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
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>