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.\" ========================================================================
.\"
.IX Title "Bio::PopGen::IO::csv 3pm"
.TH Bio::PopGen::IO::csv 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::PopGen::IO::csv \-Extract individual allele data from a CSV parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
#Do not use directly, use through the Bio::PopGen::IO driver
.PP
.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 object will parse comma delimited format (\s-1CSV\s0) or whatever
delimiter you specify. It currently doesn't handle the more complex
quote escaped \s-1CSV\s0 format.  There are 3 initialization parameters, 
the delimiter (\-field_delimiter) [default ','], (\-allele_delimiter) 
[default ' '].    The third initialization parameter is a boolean 
\&\-no_header which specifies if there is no header line to read in.  All lines starting with '#' will be skipped
.PP
When no_header is not specific the data is assumed to be of the following form.
Having a header line this
\&\s-1SAMPLE,MARKERNAME1,MARKERNAME2,...\s0
.PP
and each data line having the form (diploid data)
\&\s-1SAMP1,101 102,100 90\s0,a b
or for haploid data
\&\s-1SAMP1,101,100\s0,a
.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 "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Matthew Hahn, matthew.hahn\-at\-duke.edu
.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 8
\& Title   : new
\& Usage   : my $obj = Bio::PopGen::IO::csv\->new();
\& Function: Builds a new Bio::PopGen::IO::csv object 
\& Returns : an instance of Bio::PopGen::IO::csv
\& Args    : [optional, these are the current defaults] 
\&           \-field_delimiter => \*(Aq,\*(Aq
\&           \-allele_delimiter=> \*(Aq\es+\*(Aq
\&           \-no_header       => 0,
.Ve
.SS "flag"
.IX Subsection "flag"
.Vb 7
\& Title   : flag
\& Usage   : $obj\->flag($flagname,$newval)
\& Function: Get/Set the flag value
\& Returns : value of a flag (a boolean)
\& Args    : A flag name, currently we expect 
\&           \*(Aqno_header\*(Aq, \*(Aqfield_delimiter\*(Aq, or \*(Aqallele_delimiter\*(Aq 
\&           on set, new value (a boolean or undef, optional)
.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 $ind = $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 file 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 file format
\& Returns : none
\& Args    : L<Bio::PopGen::PopulationI> object(s)
\& Note    : Many implementation will not implement this
.Ve