File Coverage

blib/lib/BioX/SeqUtils/Promoter/Alignment.pm

Criterion	Covered	Total	%
statement	3	3	100.0
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	4	4	100.0

package BioX::SeqUtils::Promoter::Alignment;
####################################################################
#	               Charles Stephen Embry			   #
#	            MidSouth Bioinformatics Center		   #
#	        University of Arkansas Little Rock	           #
####################################################################
use base qw(BioX::SeqUtils::Promoter::Base);
use Class::Std;
use Class::Std::Utils;
use BioX::SeqUtils::Promoter::Sequences;
use BioX::SeqUtils::Promoter::Annotations;
use BioX::SeqUtils::Promoter::Annotations::Consensus;
use BioX::SeqUtils::Promoter::SaveTypes;
use warnings;
use strict;
use Carp;
use Bio::Perl;
use Bio::Seq;
use Bio::SeqIO;
use Bio::Tools::Run::Alignment::TCoffee;

use version; our $VERSION = qv('0.1.1');

{
        my %sequences_of  :ATTR( :get   :set   :default<''>    :init_arg );

        sub BUILD {
                my ($self, $ident, $arg_ref) = @_;


                return;
        }

        sub START {
                my ($self, $ident, $arg_ref) = @_;
		my $sequences = BioX::SeqUtils::Promoter::Sequences->new();
		$self->set_sequences($sequences);
                return;
        }

        sub annotate {
                my ($self,  $arg_ref) = @_;
		my $filename = defined $arg_ref->{filename} ?  $arg_ref->{filename} : '';
		my $annotations = BioX::SeqUtils::Promoter::Annotations->new({type => 'Consensus', motifs => $self->get_default_motifs() });
		$annotations->print_motifs();

                return;
        }

        sub m_align {
                my ($self,  $arg_ref) = @_;
		#a file of fasta sequences will be a parameter
		my $afilename = defined $arg_ref->{afilename} ?  $arg_ref->{afilename} : '';
		#matrix used multiple alignment, can be Pam, Blosum or none
		my $matrix = defined $arg_ref->{matrix} ?  $arg_ref->{matrix} : '';
		#the pentaly for opening a gap in the alignment
		my $gap_open = defined $arg_ref->{gap_open} ?  $arg_ref->{gap_open} : '';
		#the pentaly for exiting a gap
		my $gap_ext = defined $arg_ref->{gap_ext} ?  $arg_ref->{gap_ext} : '';
		#name and location of output file
 		my $outfile = '/home/stephen/BioCapstone/BioX-SeqUtils-Promoter/data/tnrab1000';
		# Build a tcoffee alignment factory
		#my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', 'OUTFILE' => tnrab1000.aln );
		my @params = ('ktuple' => 2, 'matrix' => $matrix, 'GAPOPEN' => $gap_open, 'GAPEXT' => $gap_ext, 'OUTFILE' => $outfile);
		#my @params = ('ktuple' => 2, 'matrix' => 'Pam', 'GAPOPEN' => 10, 'GAPEXT' => 2, 'OUTFILE' => p_GO10GE2_hexr );
		#my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', 'OUTFILE' => $outfile);
		# feed a list of parameters to Tcoffee
		my $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
		# Pass the factory a list of sequences to be aligned.
		# $aln is a SimpleAlign object.
		my $aln = $factory->align($afilename);

		return;
       }

        sub load_alignmentfile {
                my ($self,  $arg_ref) = @_;
		#load a output file from a multiple sequence alignment
		my $filename = defined $arg_ref->{filename} ?  $arg_ref->{filename} : '';
		my $text;
		#my $line;
		my $sequences = $self->get_sequences();

		open(IN,"<$filename");

		# takes each gene name and uses it as a key for a hash and the data for teh values
		;
		while($text = ){
		   	if($text) {
		   		#if($text =~/^$|^\s/){print "blank line\n"; next;}
		   		if($text =~/^$|^\s/){next;}
				my ($key, $value) = split /\s+/, $text;
				$sequences->add_segment({label => $key, sequence => $value});
			}
		}
		my $seqs = $sequences->get_sequences();
		foreach my $key (keys %$seqs ){ print $seqs->{$key}->get_sequence(),"\n"; }

                return;
        }

}

1; # Magic true value required at end of module
__END__