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