Bio::PopGen Utilities
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Summary
Bio::PopGen::Utilities - Utilities for working with PopGen data and objects
Package variables
No package variables defined.
Included modules
Bio::Align::DNAStatistics
Bio::PopGen::Individual
Bio::PopGen::Population
Inherit
Bio::Root::Root
Synopsis
  use Bio::PopGen::Utilities;
use Bio::AlignIO;
my $in = Bio::AlignIO->new(-file => 't/data/t7.aln', -format => 'clustalw'); my $aln = $in->next_aln; # get a population, each sequence is an individual and # for the default case, every site which is not monomorphic # is a 'marker'. Each individual will have a 'genotype' for the # site which will be the specific base in the alignment at that # site my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln); # get the synonymous sites from the alignemt only as the 'genotypes' # for the population my $synpop = Bio::PopGen::Utilities->aln_to_population(-site_model => 'cod', -alignment => $aln);
Description
This object provides some convience function to turn sequence
alignments into usable objects for the Population genetics modules
(Bio::PopGen).
Methods
aln_to_populationDescriptionCode
Methods description
aln_to_populationcode    nextTop
 Title   : aln_to_population
Usage : my $pop = Bio::PopGen::Utilities->aln_to_population($aln);
Function: Turn and alignment into a set of Bio::PopGen::Individual
objects grouped in a Bio::PopGen::Population object
Sites are treated as 'Markers' in the Bioperl PopGen object model in the sense that a site is a unique location for which an individual will have a genotype (a set of alleles). In this implementation we are assuming that each individual has a single entry in the alignment file. Specify a site model as one of those listed 'all' -- every base in the alignment is considered a site 'cod' -- codons The option -site_model for All sites : 'all' Codon sites : 'cod' or 'codon' To see all sites, including those which are fixed in the population add -include_monomorphic => 1 to the arguments Returns : Args : -include_monomorphic => 1 to specify all sites, even those which are monomorphic in the population (useful for HKA test mostly) [default is false] -phase => specify a phase for the data, this is only used if the site_mode is codon [default is 0] -site_model => one-of 'all', 'codon' to specify a site model for the data extraction from the alignment [default is all] -alignment => provide a Bio::SimpleAlign object [required]
Methods code
aln_to_populationdescriptionprevnextTop
sub aln_to_population {
   my ($self,@args) = @_;
   my ($aln,
       $sitemodel,$phase,
       $includefixed,$checkisa) = $self->_rearrange([qw(ALIGNMENT
				                     SITE_MODEL
					             PHASE
					             INCLUDE_MONOMORPHIC
					             CHECKISA)],
					  @args);

   my %ambig_code = ('?' => ['?','?'],
		     'N' => ['?','?'],
		     '-' => ['?','?'],
                     'G' => ['G','G'],
                     'A' => ['A','A'],
                     'T' => ['T','T'],
                     'C' => ['C','C'],
                     'R' => ['A','G'],
                     'Y' => ['C','T'],
                     'W' => ['T','A'],
                     'M' => ['C','A'],
                     'S' => ['C','G'],
                     'K' => ['G','T']);
					  
   if( ! defined $aln ) { 
       $self->warn("Must provide a valid Bio::SimpleAlign object to run aln_to_population");
       return;
   }

   if( ! $aln->is_flush ) {
       $self->warn("Must provide a Bio::SimpleAlign object with aligned sequences to aln_to_population!");
       return;
   }
   $phase = 0 unless defined $phase;
   if( $phase != 0 && $phase != 1 && $phase != 2 ) { 
       warn("phase must be 0,1, or 2");
       return;
   }
   my $alength = $aln->length;
   my @inds;
   if( ! defined $sitemodel || $sitemodel =~ /all/i ) {
       my $ct = 0;       
       my @seqs;
       for my $seq ( $aln->each_seq ) {
	   push @seqs, $seq->seq;
	   push @inds, Bio::PopGen::Individual->new(-unique_id => $seq->display_id);
       }

       for( my $i = 0; $i < $alength; $i++ ) {
	   my (@genotypes,%set);
	   
           # do we skip indels?
# slicing vertically
for my $seq ( @seqs ) { my $site = uc(substr($seq,$i,1)); push @genotypes, $ambig_code{$site}; $set{$site}++; } if( keys %set > 1 || $includefixed ) { my $genoct = scalar @genotypes; for( my $j = 0; $j < $genoct; $j++ ) { $inds[$j]->add_Genotype(Bio::PopGen::Genotype->new (-marker_name => ($i+1), -individual_id=> $inds[$j]->unique_id, -alleles => $genotypes[$j])); } } } } elsif( $sitemodel =~ /cod(on)?/i ) { my $ct = 0; my @seqs; for my $seq ( $aln->each_seq ) { push @seqs, $seq->seq; push @inds, Bio::PopGen::Individual->new(-unique_id => $seq->display_id); } my $codonct = 0; for( my $i = $phase; $i < $alength; $i += CodonLen ) { my (@genotypes,%set,$genoct); for my $seq ( @seqs ) { my @unambig_site; my $site = uc(substr($seq,$i,CodonLen)); if( length($site) < CodonLen ) { # at end of alignment and this is not in phase
$self->debug("phase was $phase, but got to end of alignment with overhang of $site"); next; } # do we check for gaps/indels here?
for (my $pos=0; $pos<CodonLen; $pos++) { $unambig_site[0] .= $ambig_code{substr($site, $pos, 1)}[0]; $unambig_site[1] .= $ambig_code{substr($site, $pos, 1)}[1]; } push @genotypes, [@unambig_site]; $set{$site}++; } $genoct = scalar @genotypes; # do we include fixed sites? I think we should leave it to the user.
if( keys %set > 1 || $includefixed ) { for( my $j = 0; $j < $genoct; $j++ ) { $inds[$j]->add_Genotype(Bio::PopGen::Genotype->new (-marker_name => ($i/CodonLen),
-individual_id=>
$inds[$j]->unique_id,
-alleles =>
$genotypes[$j]));
} $codonct++; } } } else { $self->throw("Can only build sites based on all the data right now!"); } return Bio::PopGen::Population->new(-checkisa => 0, -source => 'alignment', -individuals=>\@ inds); } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _