.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.if !\nF .nr F 0
.if \nF>0 \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    if !\nF==2 \{\
.        nr % 0
.        nr F 2
.    \}
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "Bio::PopGen::IO 3pm"
.TH Bio::PopGen::IO 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::PopGen::IO \- Input individual,marker,allele information
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  use Bio::PopGen::IO;
\&  my $io = Bio::PopGen::IO\->new(\-format => \*(Aqcsv\*(Aq,
\&                                \-file   => \*(Aqdata.csv\*(Aq);
\&
\&  # Some IO might support reading in a population at a time
\&
\&  my @population;
\&  while( my $ind = $io\->next_individual ) {
\&      push @population, $ind;
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a generic interface to reading in population genetic data (of
which there really isn't too many standard formats).  This implementation
makes it easy to provide your own parser for the data.  You need to
only implement one function next_individual.  You can also implement 
next_population if your data has explicit information about population
memberhsip for the indidviduals.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $obj = Bio::PopGen::IO\->new();
\& Function: Builds a new Bio::PopGen::IO object 
\& Returns : an instance of Bio::PopGen::IO
\& Args    :
.Ve
.SS "format"
.IX Subsection "format"
.Vb 5
\& Title   : format
\& Usage   : $format = $stream\->format()
\& Function: Get the PopGen format
\& Returns : PopGen format
\& Args    : none
.Ve
.SS "next_individual"
.IX Subsection "next_individual"
.Vb 5
\& Title   : next_individual
\& Usage   : my $ind = $popgenio\->next_individual;
\& Function: Retrieve the next individual from a dataset
\& Returns : L<Bio::PopGen::IndividualI> object
\& Args    : none
.Ve
.SS "next_population"
.IX Subsection "next_population"
.Vb 6
\& Title   : next_population
\& Usage   : my $pop = $popgenio\->next_population;
\& Function: Retrieve the next population from a dataset
\& Returns : L<Bio::PopGen::PopulationI> object
\& Args    : none
\& Note    : Many implementation will not implement this
.Ve
.SS "write_individual"
.IX Subsection "write_individual"
.Vb 5
\& Title   : write_individual
\& Usage   : $popgenio\->write_individual($ind);
\& Function: Write an individual out in the implementation format
\& Returns : none
\& Args    : L<Bio::PopGen::PopulationI> object(s)
.Ve
.SS "write_population"
.IX Subsection "write_population"
.Vb 6
\& Title   : write_population
\& Usage   : $popgenio\->write_population($pop);
\& Function: Write a population out in the implementation format
\& Returns : none
\& Args    : L<Bio::PopGen::PopulationI> object(s)
\& Note    : Many implementation will not implement this
.Ve
.SS "newFh"
.IX Subsection "newFh"
.Vb 8
\& Title   : newFh
\& Usage   : $fh = Bio::SeqIO\->newFh(\-file=>$filename,\-format=>\*(AqFormat\*(Aq)
\& Function: does a new() followed by an fh()
\& Example : $fh = Bio::SeqIO\->newFh(\-file=>$filename,\-format=>\*(AqFormat\*(Aq)
\&           $sequence = <$fh>;   # read a sequence object
\&           print $fh $sequence; # write a sequence object
\& Returns : filehandle tied to the Bio::SeqIO::Fh class
\& Args    :
.Ve
.PP
See Bio::SeqIO::Fh
.SS "fh"
.IX Subsection "fh"
.Vb 8
\& Title   : fh
\& Usage   : $obj\->fh
\& Function:
\& Example : $fh = $obj\->fh;      # make a tied filehandle
\&           $sequence = <$fh>;   # read a sequence object
\&           print $fh $sequence; # write a sequence object
\& Returns : filehandle tied to Bio::SeqIO class
\& Args    : none
.Ve
.SS "_load_format_module"
.IX Subsection "_load_format_module"
.Vb 6
\& Title   : _load_format_module
\& Usage   : *INTERNAL Bio::PopGen::IO stuff*
\& Function: Loads up (like use) a module at run time on demand
\& Example : 
\& Returns : 
\& Args    :
.Ve
.SS "_guess_format"
.IX Subsection "_guess_format"
.Vb 6
\& Title   : _guess_format
\& Usage   : $obj\->_guess_format($filename)
\& Function:
\& Example :
\& Returns : guessed format of filename (lower case)
\& Args    :
.Ve