[Bioperl-l] Bio::SimpleAlign, uniq_seq

[Weigang Qiu]

Mark and Tristan,

I am the original instigator of the uniq_seq method. The STDERR
implementation was used so that STDOUT could be piped. But it did not
conform to bioperl convention of using the $self->debug() method. I think
that's why these lines were commented out and re-implemented using the
$self->debug method. So, turning on the debug option should give the
intended ST mapping for each sequence in stderr.

weigang

On Wed, Apr 1, 2009 at 10:28 PM, Mark A. Jensen <maj at fortinbras.us> wrote:

> Tristan--
> Strange: it looks like the prints to stderr have been commented out in the
> source (back in revision 10242; 1.6 is rev 15582). The
> two statements are easy to find in the SimpleAlign.pm uniq_seq() source;
> you can
> uncomment them to work around this.
> You are right, this is rather an unconventional way to specify an output
> option-- can Chris comment?
> Mark
> ----- Original Message ----- From: "Tristan Lefebure" <
> tristan.lefebure at gmail.com>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, April 01, 2009 11:11 PM
> Subject: [Bioperl-l] Bio::SimpleAlign, uniq_seq
>
>
>
>  Hi there,
>>
>> I'm trying to use the uniq_seq function from the Bio::SimpleAlign module.
>> Here is the description:
>>
>> Title     : uniq_seq
>> Usage     : $aln->uniq_seq():  Remove identical sequences in
>>            in the alignment.  Ambiguous base ("N", "n") and
>>            leading and ending gaps ("-") are NOT counted as
>>            differences.
>> Function  : Make a new alignment of unique sequence types (STs)
>> Returns   : 1. a new Bio::SimpleAlign object (all sequences renamed as
>> "ST")
>>            2. ST of each sequence in STDERR
>> Argument  : None
>>
>> What I'm trying to obtain is the ST composition (i.e. what is supposed to
>> go
>> to STDERR), but I see nothing...
>>
>> An example:
>>
>> --------test.fasta:
>>
>>> seq1
>>>
>> AAATTTC
>>
>>> seq2
>>>
>> CAATTTC
>>
>>> seq3
>>>
>> AAATTTC
>> -------
>>
>>
>> ----------test.pl:
>> #! /usr/bin/perl
>>
>> use strict;
>> use warnings;
>> use Bio::AlignIO;
>> use Bio::SimpleAlign;
>> use Getopt::Long;
>>
>> my $in  = Bio::AlignIO->new(-file   => 'test.fasta' ,
>>                            -format => 'fasta');
>>
>> my $out = Bio::AlignIO->new(-file   => ">test.out" ,
>>                            -format => 'fasta');
>>
>> while ( my $aln = $in->next_aln() ) {
>> my $red_aln = $aln->uniq_seq;
>>       $out->write_aln($red_aln);
>>   }
>> -------------
>>
>> If you run:
>>
>> ./test.pl &> log
>>
>> you will get nothing written into the log file... (but the test.out is OK)
>>
>> Am I missing something?
>> By the way, wouldn't it be more convenient to have the ST composition
>> returned
>> in an array?
>>
>> Thanks,
>>
>> --Tristan
>> (BioPerl 1.6)
>>
>>
>>
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>>
>>
>>
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-- 
Weigang Qiu
Department of Biological Sciences
Hunter College, City University of New York
695 Park Avenue
New York, NY 10065