[Bioperl-l] SeqIO - masked seqs

[chauser]

Hi Marc,

I updated to the current CVS and get the same error.  If I tack on a  
single valid base to the offending clone(below) SeqIO reads it.

# $Id: README,v 1.37 2005/03/01 16:56:02 amackey Exp $

o Version

  This is Bioperl version 1.5 from CVS HEAD



 >1115008E10.y1  CHROMAT_FILE: 1115008E10.y1 PHD_FILE:  
1115008E10.y1.phd.1 CHEM: term
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXX



------------- EXCEPTION  -------------
MSG: Got a sequence with no letters in it cannot guess alphabet []
STACK Bio::PrimarySeq::_guess_alphabet  
/usr/local/src/bioperl/core/Bio/PrimarySeq.pm:837
STACK Bio::Seq::SeqFastaSpeedFactory::create  
/usr/local/src/bioperl/core/Bio/Seq/SeqFastaSpeedFactory.pm:137
STACK Bio::SeqIO::fasta::next_seq  
/usr/local/src/bioperl/core/Bio/SeqIO/fasta.pm:143
STACK main::RAW ESTcount.pl:81
STACK toplevel ESTcount.pl:49


Chuck



On Mar 16, 2005, at 2:16 AM, Marc Logghe wrote:

>
>> All,
>>
>> I ran into a glitch when reading sets of EST reads where some
>> reads are masked in their entirety - i.e. all bases are X's.
>> Is there a way to either modify the alphabet to accept X or
>> some other solution?
>
> I was not able to trace the actual fix. But there was a thread in
> december/january about that.
> In one of the last messages Nathan was about the fix this:
> http://bioperl.org/pipermail/bioperl-l/2005-January/017829.html
>
> Brian added a comment on this alphabet() issue.
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/ 
> SeqI
> O.pm?cvsroot=bioperl
> Have you tried bioperl release 1.5.0 or bioperl-release-1-5-0-rc2 ?
> Guess it should be fixed there.
> Is bioperl-release-1-5-0-rc2 behaving better than 1.5.0 related to the
> Bio::SeqFeatureI architecture ?
> Marc
>
>
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