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Bio::SeqIO::mbsout(3) User Contributed Perl DocumentationBio::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')

perl v5.32.1			  2019-12-07		 Bio::SeqIO::mbsout(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Warren Kretzschmar | COPYRIGHT | METHODS

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