[Bioperl-l] Mutation IO

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Jan 18 02:39:31 EST 2007


Marian,

Do not try to cram too much into one class. BIC format is apparently a useful 
shorthand for some cases, but representing that in the memory using objects 
in an expandable way is an other thing.

Your example below describes an individual's diploid genotype. Putting that 
into one sequence object is not a good idea. The way to model that is to have 
a reference sequence and then define an individual that has that sequence in 
diploid or haploid (sex chromosomes) setting and list the alleles that person 
has in the reference sequence coordinate system. You might be interested in 
separating the alleles by chromosomes, too.

Representing, reporting and modelling genotype information is something that 
has been of interest for me and a group of other people for some time. An 
early draft of a web site about a genotyping standard can be found here: 
http://www.openpml.org. It being worked on heavily and more material will be 
added soon.

	-Heikki


On Thursday 18 January 2007 01:31, marian thieme wrote:
> Jason, your right, probably it is some kind of abuse of the bioperl api,
> but its a very quick way to get results, because I dont need to cope with
> replacing substrings. On the other hand, if you are using the Root.pm class
> in other scripts, it can probably cause some malfunction (inclusive crash
> of your application). Probably its no big matter to provide a filestream IO
> class which is reading/writing the sequence and translates the in/from
> IUPAC chars. But one thing I dont see at present: How would you represent
> more complex mutations, as change of few bases ? Ok here we could represent
> each position seperatly. But in the case of a mutation ? I dont know if
> there is a iupac char which treats a mutation ! Lets consider this case:
> 1.) origin of some position is a
> 2.) some individual has in one locus an a and the other is missing that
> base or perhaps both loci are missing the a. so via BIC notation you can
> write [a/_] resp. [_/_]. Any idea how to resolve this ?
>
> Marian
>
> > Von: Jason Stajich <jason at bioperl.org>
> > An: marian thieme <marian.thieme at lycos.de>
> > Betreff: Re: [Bioperl-l] Bio::Root::Root/Bio::LiveSeq::Mutation
> > Datum: Wed, 17 Jan 2007 08:40:45 -0800
> >
> > I think you are ignoring the fact that errors are thrown for a
> > reason, not just to annoy you.
> >
> > Why not store the data in Bio::Seq objects as IUPAC ambiguity codes
> > and write a special writer class in Bio::SeqIO which converts the
> > ambiguity codes to your specified encoding.
> > There are examples of how to write your own Bio::SeqIO class in the
> > HOWTO tutorials when we talk about extending the toolkit. There is
> > also all the code to decompose an ambiguity code into the bases it
> > represents.
> >
> >
> > -jason
> >
> > On Jan 16, 2007, at 2:20 AM, marian thieme wrote:
> > > Hi, as I told to this list some time ago, I want to ouput
> > > heterozygous dna sequences of different individuals.
> > > We need to output variations in the following manner:
> > > [a/g] if there is a loci where one allele has an "a" and the other
> > > has a "g". (Also known as BIC db format or something like this)
> > > My approach is to use the Bio::LiveSeq::Mutation (class ?) to
> > > change the specific position in the sequence.
> > >
> > >
> > > Bio::SeqUtils->mutate($seqobj, Bio::LiveSeq::Mutation->new(
> > >   -seq => "[a/g]",
> > >   -seqori => $seqori,
> > >   -pos => $pos,
> > >   -len => $length));
> > >
> > > But unfortunatly this would rise an exception, that some unexpected
> > > chars occur. Hence I went in to the code of Root.pm and made a
> > > small change: commenting out line 359 in Root.pm :
> > >
> > > if( $ERRORLOADED ) {
> > > #       print STDERR "  Calling Error::throw\n\n";
> > >
> > >        # Enable re-throwing of Error objects.
> > >        # If the error is not derived from Bio::Root::Exception,
> > >        # we can't guarantee that the Error's value was set properly
> > >        # and, ipso facto, that it will be catchable from an eval{}.
> > >        # But chances are, if you're re-throwing non-
> > > Bio::Root::Exceptions,
> > >        # you're probably using Error::try(), not eval{}.
> > >        # TODO: Fix the MSG: line of the re -thrown error. Has an
> > > extra line
> > >        # containing the '----- EXCEPTION -----' banner.
> > >        if( ref($args[0])) {
> > >            if( $args[0]->isa('Error')) {
> > >                my $class = ref $args[0];
> > >                $class->throw( @args );
> > >            } else {
> > >                my $text .= "\nWARNING: Attempt to throw a non-
> > > Error.pm object: " . ref$args[0];
> > >                my $class = "Bio::Root::Exception";
> > >                $class->throw( '-text' => $text, '-value' => $args
> > > [0] );
> > >            }
> > >        } else {
> > >            $class ||= "Bio::Root::Exception";
> > >
> > >            my %args;
> > >            if( @args % 2 == 0 && $args[0] =~ /^-/ ) {
> > >                %args = @args;
> > >                $args{-text} = $text;
> > >                $args{-object} = $self;
> > >            }
> > >
> > > (Line 359:)   #$class->throw( scalar keys %args > 0 ? %args :
> > > @args ); # (%args || @args) puts %args in scalar context!
> > >  &nbs p;     }
> > >    }
> > >
> > >
> > > After I did alter this line all is working fine. But I know that
> > > this can be considered in the best case  as a work around.
> > >
> > > 2 Questions:
> > >
> > > Do you think it is worth to provide some class which are natively
> > > able to cope with that matter ?
> > > Do I need to expect some unwanted behavior of some scripts resp.
> > > classes ?
> > >
> > > Regards,
> > > Marian
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > _________________________________
> > > Stelle Deine Fragen bei Lycos iQ <a
> >
> > href=http://iq.lycos.de/qa/ask/>http://iq.lycos.de/qa/ask/</a>>
> >
> > > _______________________________________________
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> > href=http://lists.open-bio.org/mailman/listinfo/bioperl-l>http://lists.op
> >en- bio.org/mailman/listinfo/bioperl-l</a>
> > --
> > Jason Stajich
> > Miller Research Fellow
> > University of California, Berkeley
> > lab: 510.642.8441
> > <a
> > href=http://pmb.berkeley.edu/~taylor/people/js.html>http://pmb.berkeley.e
> >du/ ~taylor/people/js.html</a>
> >
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


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