[Bioperl-l] AlignIO

[Jason Stajich]

There are other randomizing tools out there -- I believe Sean Eddy's shuffle does this

http://www.bioperl.org/wiki/SQUID#shuffle

On Jun 21, 2011, at 10:23 AM, Chad Davis wrote:

> It sounds like your randomization procedure is breaking the alignment
> format, such that the clustal parser can no longer read it. How are
> you randomizing the file? An example might help.
> 
> Chad
> 
> On Tue, Jun 21, 2011 at 18:55, ashwoo <projectbasu at gmail.com> wrote:
>> Dear All,
>>              I have a script which parses the best HSP alignment out
>> of BLAST result and writes it to a temporary file.
>> 
>> my $aln = $hsp->get_aln;
>> 1. my $out = Bio::AlignIO->new(-file => ">tmp.aln",
>> 2.                                 -format => 'clustalw');
>> 3. $out->write_aln($aln);
>> 
>> 
>> I randomize the alignment within the "tmp.aln" file to generate a new
>> file "mult_rand.aln" containing all randomized alignments in clustalw
>> format.
>> Now I want to read each alignment in the randomized file hence I use
>> 
>> 4. my $in  = Bio::AlignIO->new(-file   => "mult_rand.aln",
>> 5.                                           -format => 'clustalw');
>> 6. while ( my $aln = $in->next_aln() ) {
>> 7.   #"RUN RNAZ to check the conservedness of each randomized
>> alignment"
>> 8.   #NOT GETTING ANY VALUES HERE
>> 9.   }
>> 
>> But I am not able to access each alignment. When I open the randomized
>> aln file with a separate script and same code in lines 4-9  it works
>> fine. Is this happening due to my using AlignIO objects twice in the
>> same script. Please Help.
>> 
>> yours sincerely,
>> Perl Novice
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>> 
> 
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