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Bio::PopGen::IO::csv(3User Contributed Perl DocumentatiBio::PopGen::IO::csv(3)

NAME
       Bio::PopGen::IO::csv -Extract individual	allele data from a CSV parser

SYNOPSIS
       #Do not use directly, use through the Bio::PopGen::IO driver

	 use Bio::PopGen::IO;
	 my $io	= Bio::PopGen::IO->new(-format => 'csv',
				      -file   => 'data.csv');

	 # Some	IO might support reading in a population at a time

	 my @population;
	 while(	my $ind	= $io->next_individual ) {
	     push @population, $ind;
	 }

DESCRIPTION
       This object will	parse comma delimited format (CSV) or whatever
       delimiter you specify. It currently doesn't handle the more complex
       quote escaped CSV 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

       When no_header is not specific the data is assumed to be	of the
       following form.	Having a header	line this
       SAMPLE,MARKERNAME1,MARKERNAME2,...

       and each	data line having the form (diploid data) SAMP1,101 102,100
       90,a b or for haploid data SAMP1,101,100,a

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

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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 - Jason Stajich
       Email jason-at-bioperl.org

CONTRIBUTORS
       Matthew Hahn, matthew.hahn-at-duke.edu

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	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 => ','
		  -allele_delimiter=> '\s+'
		  -no_header	   => 0,

   flag
	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
		  'no_header', 'field_delimiter', or 'allele_delimiter'
		  on set, new value (a boolean or undef, optional)

   next_individual
	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

   next_population
	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

   write_individual
	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)

   write_population
	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

perl v5.24.1			  2017-07-08	       Bio::PopGen::IO::csv(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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