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Bio::PopGen::IO::prettUsereContributed Perl DocuBio::PopGen::IO::prettybase(3)

NAME
       Bio::PopGen::IO::prettybase - Extract individual	allele data from
       PrettyBase format

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

DESCRIPTION
       This object will	parse comma delimited PrettyBase output.  PrettyBase
       is defined by the SeattleSNPs http://pga.gs.washington.edu/

       This is expected	to be tab delimited (you can vary with the
       field_delimiter flag SITE SAMPLE	ALLELE1	ALLELE2

       There are 2 initialization parameters, the delimiter (-field_delimiter)
       [default	'tab'] and a boolean -no_header	which specifies	if there is no
       header line to read in.	All lines starting with	'#' will be skipped

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::prettybase->new();
	Function: Builds a new Bio::PopGen::IO::prettybase object
	Returns	: an instance of Bio::PopGen::IO::prettybase
	Args	: -field_delimiter	=> a field delimiter character or regexp (default is /\t/ )
		  -header		=> boolean if the file will have a header and parser should
					   skip	first line in the file (default	is false)
		  -convert_indel_states	=> convert alleles which are longer than one character
					   to an 'I' meaning insert state, and alleles which are
					   '-' to a delete state.
					   (default is false)

   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
		  '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	: 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	: 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::prettybase(3)

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

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