File Coverage

blib/lib/Bio/FASTASequence/File.pm

Criterion	Covered	Total	%
statement	12	33	36.3
branch	0	8	0.0
condition	0	4	0.0
subroutine	4	8	50.0
pod	2	3	66.6
total	18	56	32.1

package Bio::FASTASequence::File;

use 5.006001;
use strict;
use warnings;
use Bio::FASTASequence;

our $VERSION = '0.04';


# Preloaded methods go here.

sub new{
  my ($class,$filename) = @_;
  my $self = {};
  $self->{file} = $filename || '';
  _parse_file($self) if($self->{file});
  bless($self,$class);
  return $self;
}# end new

sub file{
  my ($self,$file) = @_;
  $self->{file} = $file || '';
  _parse_file($self) if($self->{file});
  return $self->{result};
}# end file

sub get_result{
  my ($self) = @_;
  return $self->{result};
}# end get_parsed

sub _parse_file{
  my ($self) = @_;
  local $/ = "\n>";
  open(FH,$self->{file}) or die($self->{file}.": ".$!);
  while(my $entry = ){
    $entry = '>'.$entry unless($entry =~ /^>/);
    $entry =~ s/>$//;
    my $seq = Bio::FASTASequence->new($entry);
    $self->{result}->{$seq->getAccessionNr()} = $seq;
  }
  close FH;
}

1;
__END__