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Bio::PopGen::IO::hapmap.3pm
Langue: en
Version: 2009-02-27 (fedora - 05/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::PopGen::IO::hapmap - A parser for HapMap output dataSYNOPSIS
# Do not use directly, use through the Bio::PopGen::IO driver use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => 'hapmap', -file => 'data.hapmap'); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push @population, $ind; }
DESCRIPTION
A driver module for Bio::PopGen::IO for parsing hapmap data.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
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:
http://bugzilla.open-bio.org/
AUTHOR - Rich Dobson
Email r.j.dobson-at-qmul.ac.ukCONTRIBUTORS
Jason Stajich, jason-at-bioperl.orgAPPENDIX
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::hapmap->new(); Function: Builds a new Bio::PopGen::IO::hapmap object Returns : an instance of Bio::PopGen::IO::hapmap Args : [optional, these are the current defaults] -field_delimiter => ',' -allele_delimiter=> '\s+' -no_header => 0, -starting_column => 11
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 : A Bio::PopGen::IndividualI object Args : none
See Bio::PopGen::IndividualI
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
See Bio::PopGen::PopulationI
write_individual
Title : write_individual Usage : $popgenio->write_individual($ind); Function: Write an individual out in the file format NOT SUPPORTED BY hapmap format Returns : none Args : Bio::PopGen::PopulationI object(s)
See Bio::PopGen::PopulationI
write_population
Title : write_population Usage : $popgenio->write_population($pop); Function: Write a population out in the file format NOT SUPPORTED BY hapmap format Returns : none Args : Bio::PopGen::PopulationI object(s) Note : Many implementation will not implement this
See Bio::PopGen::PopulationI
starting_column
Title : starting_column Usage : $obj->starting_column($newval) Function: Column where data starts Example : Returns : value of starting_column (a scalar) Args : on set, new value (a scalar or undef, optional)
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