| Bio::PopGen::IO::csv(3pm) | User Contributed Perl Documentation | Bio::PopGen::IO::csv(3pm) |
Bio::PopGen::IO::csv -Extract individual allele data from a CSV parser
#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;
}
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
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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.
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:
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Email jason-at-bioperl.org
Matthew Hahn, matthew.hahn-at-duke.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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,
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)
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
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
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)
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
| 2018-10-27 | perl v5.26.2 |