Bio::PopGen::Utilities.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::PopGen::Utilities - Utilities for working with PopGen data and objects

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).

FEEDBACK

Mailing Lists

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

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 Bugs

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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

aln_to_population

  Title   : aln_to_population
  Usage   : my $pop = Bio::PopGen::Utilities->aln_to_population($aln);
  Function: Turn and alignment into a set of L<Bio::PopGen::Individual>
            objects grouped in a L<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 L<Bio::SimpleAlign> object [required]