Bio::SeqIO::mbsout(3)

NAME
Bio::SeqIO::mbsout - input stream for output by Teshima et al.'s mbs.

SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION
mbs (Teshima KM, Innan H (2009) mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. BMC Bioinformatics 10: 166 ) can be found at http://www.biomedcentral.com/1471-2105/10/166/additional/.

Currently this object can be used to read output from mbs into seq objects. However, because bioperl has no support for haplotypes created using an infinite sites model (where '1' identifies a derived allele and '0' identifies an ancestral allele), the sequences returned by mbsout are coded using A, T, C and G. To decode the bases, use the sequence conversion table (a hash) returned by get_base_conversion_table(). In the table, 4 and 5 are used when the ancestry is unclear. This should not ever happen when creating files with mbs, but it will be used when creating mbsOUT files from a collection of seq objects ( To be added later ). Alternatively, use get_next_hap() to get a string with 1's and 0's instead of a seq object.

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

  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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Warren Kretzschmar
This module was written by Warren Kretzschmar

email: wkretzsch@gmail.com

This module grew out of a parser written by Aida Andres.

COPYRIGHT

  Public Domain Notice
This software/database is ``United States Government Work'' under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus cannot be copyrighted. This software/database is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose.

METHODS

  INTERNAL METHODS
_initialize

Title : _initialize Usage : $stream = Bio::SeqIO::mbsout->new($infile) Function: extracts basic information about the file. Returns : Bio::SeqIO object Args : no_og
Details    : include 'no_og' flag = 0 if the last population of an mbsout file
          contains only one haplotype and you want the last haplotype to be
          treated as the outgroup.

_read_start

Title : _read_start Usage : $stream->_read_start() Function: reads from the filehandle $stream->{_filehandle} all information up to the first haplotype (sequence). Returns : void Args : none

  Methods to retrieve mbsout data
get_segsites

Title : get_segsites Usage : $segsites = $stream->get_segsites() Function: returns the number segsites in the mbsout file (according to the mbsout header line). Returns : scalar Args : NONE

get_current_run_segsites

Title : get_current_run_segsites Usage : $segsites = $stream->get_current_run_segsites() Function: returns the number of segsites in the run of the last read haplotype (sequence). Returns : scalar Args : NONE

get_pop_mut_param_per_site

Title : get_pop_mut_param_per_site Usage : $pop_mut_param_per_site = $stream->get_pop_mut_param_per_site() Function: returns 4*N0*mu or the "population mutation parameter per site" Returns : scalar Args : NONE

get_pop_recomb_param_per_site

Title : get_pop_recomb_param_per_site Usage : $pop_recomb_param_per_site = $stream->get_pop_recomb_param_per_site() Function: returns 4*N0*r or the "population recombination parameter per site" Returns : scalar Args : NONE

get_nsites

Title : get_nsites Usage : $nsites = $stream->get_nsites() Function: returns the number of sites simulated by mbs. Returns : scalar Args : NONE

get_selpos

Title : get_selpos Usage : $selpos = $stream->get_selpos() Function: returns the location on the chromosome where the allele is located that was selected for by mbs. Returns : scalar Args : NONE

get_nreps

Title : get_nreps Usage : $nreps = $stream->get_nreps() Function: returns the number replications done by mbs on each trajectory file to create the mbsout file. Returns : scalar Args : NONE

get_nfiles

Title : get_nfiles Usage : $nfiles = $stream->get_nfiles() Function: returns the number of trajectory files used by mbs to create the mbsout file Returns : scalar Args : NONE

get_traj_filename

Title : get_traj_filename Usage : $traj_filename = $stream->get_traj_filename() Function: returns the prefix of the trajectory files used by mbs to create the mbsout file Returns : scalar Args : NONE

get_runs

Title : get_runs Usage : $runs = $stream->get_runs() Function: returns the number of runs in the mbsout file Returns : scalar Args : NONE

get_Positions

Title : get_Positions Usage : @positions = $stream->get_Positions() Function: returns an array of the names of each segsite of the run of the last read hap. Returns : array Args : NONE

get_tot_run_haps

Title : get_tot_run_haps Usage : $number_of_haps_per_run = $stream->get_tot_run_haps() Function: returns the number of haplotypes (sequences) in each run of the mbsout file. Returns : scalar >= 0 Args : NONE

get_mbs_info_line

Title : get_mbs_info_line Usage : $mbs_info_line = $stream->get_mbs_info_line() Function: returns the header line of the mbsout file. Returns : scalar Args : NONE

tot_haps

Title : tot_haps Usage : $number_of_haplotypes_in_file = $stream->tot_haps() Function: returns the number of haplotypes (sequences) in the mbsout file. Information gathered from mbsout header line. Returns : scalar Args : NONE

next_run_num

Title : next_run_num Usage : $next_run_number = $stream->next_run_num() Function: returns the number of the mbs run that the next haplotype (sequence)
          will be taken from (starting at 1). Returns undef if the complete
          file has been read. Returns : scalar > 0 or undef Args : NONE

get_last_haps_run_num

Title : get_last_haps_run_num Usage : $last_haps_run_number = $stream->get_last_haps_run_num() Function: returns the number of the ms run that the last haplotype (sequence)
          was taken from (starting at 1). Returns undef if no hap has been
          read yet. Returns : scalar > 0 or undef Args : NONE

get_last_read_hap_num

Title : get_last_read_hap_num Usage : $last_read_hap_num = $stream->get_last_read_hap_num()
          Function: returns the number (starting with 1) of the last haplotype
          read from the mbs file Returns : scalar >= 0 Args : NONE
Details    : 0 means that no haplotype has been read yet.

outgroup

Title : outgroup Usage : $outgroup = $stream->outgroup() Function: returns '1' if the mbsout object has an outgroup. Returns '0'
          otherwise. Returns : 1 or 0, currently always 0 Args : NONE
Details    : This method will return '1' only if the last population in the mbsout
          file contains only one haplotype. If the last population is not an
          outgroup then create the mbsout object using 'no_outgroup' as input
          parameter for new() (see mbsout->new()).

          Currently there exists no way of introducing an outgroup into an mbs
          file, so this function will always return '0'.

get_next_seq

Title : get_next_seq Usage : $seq = $stream->get_next_seq() Function: reads and returns the next sequence (haplotype) in the stream Returns : Bio::Seq object Args : NONE
Note    : This function is included only to conform to convention.  It only
          calls next_hap() and passes on that method's return value. Use
          next_hap() instead for better performance.

get_next_hap

Title : get_next_hap Usage : $seq = $stream->get_next_hap() Function: reads and returns the next sequence (haplotype) in the stream. Returns
          void if all sequences in stream have been read. Returns : Bio::Seq object Args : NONE
Note    : Use this instead of get_next_seq().

get_next_run

Title : get_next_run Usage : @seqs = $stream->get_next_run() Function: reads and returns all the remaining sequences (haplotypes) in the mbs
          run of the next sequence. Returns : array of Bio::Seq objects Args : NONE

  METHODS TO RETRIEVE CONSTANTS
base_conversion_table

Title : get_base_conversion_table Usage : $table_hash_ref = $stream->get_base_conversion_table() Function: returns a reference to a hash. The keys of the hash are the letters
          'A','T','G','C'. The values associated with each key are the value
          that each letter in the sequence of a seq object returned by a
          Bio::SeqIO::mbsout stream should be translated to. Returns : reference to a hash Args : NONE Synopsis:

        # retrieve the Bio::Seq object's sequence
        my $haplotype = $seq->seq;
        my $rh_base_conversion_table = $stream->get_base_conversion_table();

        # need to convert all letters to their corresponding numbers.
        foreach my $base (keys %{$rh_base_conversion_table}){
                $haplotype =~ s/($base)/$rh_base_conversion_table->{$base}/g;
        }

        # $haplotype is now an ms style haplotype. (e.g. '100101101455')