Bio::PopGen::IO::csv(3User Contributed Perl DocumentatiBio::PopGen::IO::csv(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::PopGen::IO::csv(3)
