Bio::SeqIO::msout(3) input stream for output by Hudson's ms

SYNOPSIS

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

DESCRIPTION

ms ( Hudson, R. R. (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-8 ) can be found at http://home.uchicago.edu/~rhudson1/source/mksamples.html.

Currently, this object can be used to read output from ms 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 msout 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 ms, but it will be used when creating msOUT 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.

Mapping to Finite Sites

This object can now also be used to map haplotypes created using an infinite sites model to sequences of arbitrary finite length. See set_n_sites() for more detail. Thanks to Filipe G. Vieira <[email protected]> for the idea and code.

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. 

  [email protected]                  - General discussion
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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: [email protected]

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

Methods for Internal Use

_initialize

Title : _initialize Usage : $stream = Bio::SeqIO::msOUT->new($infile) Function: extracts basic information about the file. Returns : Bio::SeqIO object Args : no_og, gunzip, gzip, n_sites Details :

    - include 'no_og' flag if the last population of an msout file contains
      only one haplotype and you don't want the last haplotype to be
      treated as the outgroup ( suggested when reading data created by ms ).
    - including 'n_sites' (positive integer) causes all output haplotypes to be
      mapped to a sequence of length 'n_sites'. See set_n_sites() for more details.

_read_start

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

Methods to Access Data

get_segsites

Title : get_segsites Usage : $segsites = $stream->get_segsites() Function: returns the number of segsites in the msOUT file (according to the msOUT header line's -s option), or the current run's segsites if -s was not specified in the command line (in this case the number of segsites varies from run to run). 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_n_sites

Title : get_n_sites Usage : $n_sites = $stream->get_n_sites() Function: Gets the number of total sites (variable or not) to be output. Returns : scalar if n_sites option is defined at call time of new() Args : NONE Note :
          WARNING: Final sequence length might not be equal to n_sites if n_sites is
                   too close to number of segregating sites in the msout file.

set_n_sites

Title : set_n_sites Usage : $n_sites = $stream->set_n_sites($value) Function: Sets the number of total sites (variable or not) to be output. Returns : 1 on success; throws an error if $value is not a positive integer or undef Args : positive integer Note :
          WARNING: Final sequence length might not be equal to n_sites if it is 
                   too close to number of segregating sites.
          - n_sites needs to be at least as large as the number of segsites of 
            the next haplotype returned
          - n_sites may also be set to undef, in which case haplotypes are returned 
            under the infinite sites model assumptions.

get_runs

Title : get_runs Usage : $runs = $stream->get_runs() Function: returns the number of runs in the msOUT file (according to the
          msinfo line) Returns : scalar Args : NONE

get_Seeds

Title : get_Seeds Usage : @seeds = $stream->get_Seeds() Function: returns an array of the seeds used in the creation of the msOUT file. Returns : array Args : NONE Details : In older versions, ms used three seeds. Newer versions of ms seem to
          use only one (longer) seed.  This function will return all the seeds
          found.

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 Details : The Positions may or may not vary from run to run depending on the
          options used with ms.

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 msOUT
          file ( according to the msinfo line ). Returns : scalar >= 0 Args : NONE Details : This number should not vary from run to run.

get_ms_info_line

Title : get_ms_info_line Usage : $ms_info_line = $stream->get_ms_info_line() Function: returns the header line of the msOUT 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 msOUT file.
          Information gathered from msOUT header line. Returns : scalar Args : NONE

get_Pops

Title : get_Pops Usage : @pops = $stream->pops() Function: returns an array of population sizes (order taken from the -I flag in
          the msOUT header line).  This array will include the last hap even if
          it looks like an outgroup. Returns : array of scalars > 0 Args : NONE

get_next_run_num

Title : get_next_run_num Usage : $next_run_number = $stream->next_run_num() Function: returns the number of the ms 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 ms file Returns : scalar >= 0 Args : NONE Details : 0 means that no haplotype has been read yet. Is reset to 0 every run.

outgroup

Title : outgroup Usage : $outgroup = $stream->outgroup() Function: returns '1' if the msOUT stream has an outgroup. Returns '0'
          otherwise. Returns : '1' or '0' Args : NONE Details : This method will return '1' only if the last population in the msOUT

          file contains only one haplotype.  If the last population is not an
          outgroup then create the msOUT object using 'no_og' as input flag.
          Also, return 0, if the run has only one population.

get_next_haps_pop_num

Title : get_next_haps_pop_num Usage : ($next_haps_pop_num, $num_haps_left_in_pop) = $stream->get_next_haps_pop_num() Function: First return value is the population number (starting with 1) the
          next hap will come from. The second return value is the number of haps
          left to read in the population from which the next hap will come. Returns : (scalar > 0, scalar > 0) Args : NONE

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 or void if end of file Args : NONE Note    : This function is included only to conform to convention. The

          returned Bio::Seq object holds a halpotype in coded form. Use the hash
          returned by get_base_conversion_table() to convert 'A', 'T', 'C', 'G'
          back into 1,2,4 and 5. Use get_next_hap() to retrieve the halptoype as
          a string of 1,2,4 and 5s instead.

next_seq

Title : next_seq Usage : $seq = $stream->next_seq() Function: Alias to get_next_seq() Returns : Bio::Seq object or void if end of file Args : NONE Note : This function is only included for convention. It calls get_next_seq().
          See get_next_seq() for details.

get_next_hap

Title : get_next_hap Usage : $hap = $stream->next_hap() Function: reads and returns the next sequence (haplotype) in the stream.
          Returns undef if all sequences in stream have been read. Returns : Haplotype string (e.g. '110110000101101045454000101' Args : NONE Note    : Use get_next_seq() if you want the halpotype returned as a

          Bio::Seq object.

get_next_pop

Title : get_next_pop Usage : @seqs = $stream->next_pop() Function: reads and returns all the remaining sequences (haplotypes) in the
          population of the next sequence.  Returns an empty list if no more 
          haps remain to be read in the stream   Returns : array of Bio::Seq objects Args : NONE

next_run

Title : next_run Usage : @seqs = $stream->next_run() Function: reads and returns all the remaining sequences (haplotypes) in the ms
          run of the next sequence.  Returns an empty list if all haps have been
          read from the stream.   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::msout stream should be translated to. Returns : reference to a hash Args : NONE Synopsys: 

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

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