test.pl

#!/usr/bin/perl

use warnings;
use strict;

use lib 'lib';
#did it work
use Carp;
use Data::Dumper;
use DBI;
use English qw(-no_match_vars);
use Exception::Class;
use IPlant::TreeRec;
use IPlant::TreeRec::BlastArgs;
use IPlant::TreeRec::BlastSearcher;
use IPlant::TreeRec::DatabaseTreeLoader;
use IPlant::TreeRec::FileRetriever;
use IPlant::TreeRec::FileTreeLoader;
use IPlant::TreeRec::GeneFamilyInfo;
use IPlant::TreeRec::GeneTreeEvents;
use IPlant::TreeRec::SpeciesTreeEvents;
use JSON qw();
use Perl6::Slurp;

use constant PASSWORD_FILE => "$ENV{HOME}/mysql.tr_searcher";

local $Data::Dumper::Useqq = 1;

# Establish the database connection.
my $dsn      = "DBI:mysql:database=tree_reconciliation";
my $user     = "tr_searcher";
my $password = load_password();
my $dbh      = IPlant::DB::TreeRec->connect( $dsn, $user, $password );


# Create the tree loader.
#my $tree_loader = IPlant::TreeRec::FileTreeLoader->new(
#    {   data_dir           => '/home/dennis/treerec/clusters',
#        filename_extension => '_genetree.nhx',
#        tree_format        => 'nhx',
#    }
#);
my $tree_loader = IPlant::TreeRec::DatabaseTreeLoader->new($dbh);

# Create the gene family info.
my $gene_family_info = IPlant::TreeRec::GeneFamilyInfo->new(
    {   dbh                  => $dbh,
        go_term_length_limit => 30,
    }
);

# Create the file retriever.
my $file_retriever = IPlant::TreeRec::FileRetriever->new(
    { data_dir => '/home/dennis/treerec/clusters' } );

# Create the BLAST searcher.
my $blast_searcher = IPlant::TreeRec::BlastSearcher->new(
    {   executable_dir => '/usr/bin',
        database_dir   => '/home/dennis/treerec/blastdb',
    }
);

# Create the gene tree decorations
my $gene_tree_events = IPlant::TreeRec::GeneTreeEvents->new(
	{	  dbh                  => $dbh,		
	}
);

# Create the species tree decorations
my $species_tree_events = IPlant::TreeRec::SpeciesTreeEvents->new(
	{	  dbh                  => $dbh,		
	}
);


# Create the tree reconciliation object.
my $treerec = IPlant::TreeRec->new(
    {   dbh              => $dbh,
        gene_tree_loader => $tree_loader,
        gene_family_info => $gene_family_info,
        file_retriever   => $file_retriever,
        blast_searcher   => $blast_searcher,
        gene_tree_events =>$gene_tree_events,
        species_tree_events =>$species_tree_events,
        
    }
);


eval {
    # warn Dumper $treerec->go_search("miRNA binding");
    # warn Dumper $treerec->go_accession_search("0031124");
    # warn Dumper $treerec->gene_id_search("V01G0907");
    # warn Dumper $treerec->get_gene_family_details('pg13389',0);#'pg17605',0);'pg07475'
  # warn Dumper $treerec->get_gene_tree_events('pg13389',0);
 #
 #   warn Dumper $treerec->get_species_tree_events('pg13389',0);
#    warn Dumper $treerec->get_rec('pg13389',0);
#    warn Dumper $treerec->get_gene_family_summary("pg00921");
#     warn Dumper $treerec->get_gene_family_summary("pg00892");
  #  warn Dumper $treerec->get_gene_family_details('pg13389',0);
    # warn Dumper get_gene_tree_file( $treerec, 'pg13389' );
   #  warn Dumper get_gene_tree_file( $treerec, 'pg00892', 'bowers_rosids' );
    # warn Dumper get_species_tree_file( $treerec, 'bowers_rosids' );
    # warn Dumper get_species_tree_file( $treerec, 'bowers_rosids', 'pg00892' );
  #      warn Dumper _get_gene_tree_data( $treerec, 'pg07475',0 );
 #    warn Dumper _get_gene_tree_data( $treerec, 'pg00892', 0 );
  #  warn Dumper _get_species_tree_data($treerec,0, 'pg13389');
    # warn Dumper get_species_tree_data( $treerec, 'bowers_rosids', 'pg00892' );

    # warn Dumper $treerec->resolve_reconciliations(
    #     JSON->new()->encode(
    #         {   'speciesTreeName' => 'bowers_rosids',
    #             'familyName'      => 'pg00892',
    #             'speciesTreeNode' => 8,
    #             'edgeSelected'    => 0,
    #         }
    #     )
    # );
    # warn Dumper $treerec->resolve_reconciliations(
    #     JSON->new()->encode(
    #         {   'speciesTreeName' => 'bowers_rosids',
    #             'familyName'      => 'pg00892',
    #             'speciesTreeNode' => 8,
    #             'edgeSelected'    => 1,
    #         }
    #     )
    # );
    # warn Dumper $treerec->resolve_reconciliations(
    #     JSON->new()->encode(
    #         {   'speciesTreeName' => 'bowers_rosids',
    #             'familyName'      => 'pg00892',
    #             'geneTreeNode'    => 8,
    #         }
    #     )
    # );

    # for my $type ( $file_retriever->get_file_types() ) {
    #     warn Dumper $treerec->get_file( $type, 'pg00892' );
    # }

    # warn Dumper blast_search( $treerec, 'nucleotide', 'dna_query.fa' );
    # warn Dumper blast_search( $treerec, 'protein', 'protein_query.fa' );
 #   warn Dumper blast_search( $treerec, 'protein', 'protein_query_pg00921.fa' );
    # warn Dumper find_duplication_events( $treerec, 10, 1 );
     warn Dumper find_duplication_events( $treerec, 10, 1 );
};
if ( my $e = Exception::Class->caught() ) {
    warn "Exception: $e";
    if ( ref $e ) {
        warn $e->trace()->as_string();
    }
}

exit;

##########################################################################
# Usage      : $dbh = connect( $dsn, $user, $password );
#
# Purpose    : Establishes the database connection.
#
# Returns    : The database handle.
#
# Parameters : $dsn      - the data source name.
#              $user     - the username used to access the database.
#              $password - the password used to access the database.
#
# Throws     : IPlant::TreeRec::DatabaseException
sub connect {
    my ( $dsn, $user, $password ) = @_;

    # Establish the database connection.
    my $dbh = IPlant::DB::TreeRec->connect( $dsn, $user, $password );
    IPlant::TreeRec::DatabaseException->throw( error => DBI::errstr )
        if !defined $dbh;

    return $dbh;
}

##########################################################################
# Usage      : $password = load_password();
#
# Purpose    : Loads the password from the password file.
#
# Returns    : The password.
#
# Parameters : None.
#
# Throws     : "unable to open $file for input: $reason"
#              "unable to close $file: $reason"
sub load_password {
    my $file = PASSWORD_FILE;

    # Open the file.
    open my $in, '<', $file
        or croak "unable to open $file for input: $ERRNO";

    # Load the contents of the file.
    my $password = do { local $\; <$in> };

    # Close the file.
    close $in
        or croak "unable to close $file: $ERRNO";

    return $password;
}

##########################################################################
# Usage      : $results_ref = blast_search( $treerec, $type, $file );
#
# Purpose    : Performs a BLAST search.
#
# Returns    : The results of the BLAST search.
#
# Parameters : $treerec - an instance of IPlant::TreeRec.
#              $type    - the type of sequence (nucleotide or protein).
#              $file    - the name of the file containing the sequence.
#
# Throws     : No exceptions.
sub blast_search {
    my ( $treerec, $type, $file ) = @_;

    # Build the BLAST arguments JSON.
    my $blast_args_json = JSON->new()->encode(
        {   sequenceType => $type,
            sequence     => scalar slurp $file,
        }
    );

    #Perform the search.
    return $treerec->blast_search($blast_args_json);
}

##########################################################################
# Usage      : $results_ref = find_duplication_events( $treerec,
#                  $node_id, $edge_selected );
#
# Purpose    : Finds gene family names with duplication events in a
#              specific point in a species tree.
#
# Returns    : A reference to a list of gene family names.
#
# Parameters : $treerec       - an instance of IPlant::TreeRec.
#              $node_id       - the node identifier.
#              $edge_selected - true if the edge is selected.
#
# Throws     : No exceptions.
sub find_duplication_events {
    my ( $treerec, $node_id, $edge_selected ) = @_;

    # Build the arguments JSON.
    my $edge_selected_json = $edge_selected ? JSON::true : JSON::false;
    my $json = JSON->new()->encode(
        {   nodeId       => $node_id,
            edgeSelected => $edge_selected_json,
        }
    );

    # Perform the search.
    return $treerec->find_duplication_events($json);
}

##########################################################################
# Usage      : $results_ref = get_gene_tree_data( $treerec, $family_name,
#                  $species_tree_name );
#
# Purpose    : Gets the gene tree data for the given gene family name
#              and, optionally, for the given species tree name.
#
# Returns    : A reference to the gene tree data.
#
# Parameters : $treerec           - an instance of IPlant::TreeRec.
#              $family_name       - the gene family name.
#              $species_tree_name - the name of the species tree.
#
# Throws     : IPlant::TreeRec::GeneFamilyNotFoundException
#              IPlant::TreeRec::TreeNotFoundException
#              IPlant::TreeRec::ReconciliationNotFoundException
#              IPlant::TreeRec::IllegalArgumentException
sub _get_gene_tree_data {
    my ( $treerec, $family_name, $reconciliation_set_id ) = @_;
    my $json = build_tree_args( $family_name, $reconciliation_set_id );
    return $treerec->get_gene_tree_data($json);
}


##########################################################################
# Usage      : $results_ref = get_gene_tree_decorations( $treerec, $family_name,
#                  $species_tree_name );
#
# Purpose    : Gets the gene tree decorations for the given gene family name
#              and, optionally, for the given species tree name.
#
# Returns    : A reference to the gene tree data.
#
# Parameters : $treerec           - an instance of IPlant::TreeRec.
#              $family_name       - the gene family name.
#              $species_tree_name - the name of the species tree.
#
# Throws     : IPlant::TreeRec::GeneFamilyNotFoundException
#              IPlant::TreeRec::TreeNotFoundException
#              IPlant::TreeRec::ReconciliationNotFoundException
#              IPlant::TreeRec::IllegalArgumentException
#sub get_gene_tree_decorations {
#    my ( $treerec, $family_name, $species_tree_name ) = @_;
#    my $json = build_tree_args( $family_name, $species_tree_name );
#    return $treerec->get_gene_tree_decorations($json);
#}

##########################################################################
# Usage      : $results_ref = get_gene_tree_file( $treerec, $family_name,
#                  $species_tree_name );
#
# Purpose    : Gets the gene tree file information for the given gene
#              family name and, optionally, for the given species tree
#              name.
#
# Returns    : A reference to the gene tree data.
#
# Parameters : $treerec           - an instance of IPlant::TreeRec.
#              $family_name       - the gene family name.
#              $species_tree_name - the name of the species tree.
#
# Throws     : IPlant::TreeRec::GeneFamilyNotFoundException
#              IPlant::TreeRec::TreeNotFoundException
#              IPlant::TreeRec::ReconciliationNotFoundException
#              IPlant::TreeRec::IllegalArgumentException
sub get_gene_tree_file {
    my ( $treerec, $family_name, $species_tree_name ) = @_;
    my $json = build_tree_args( $family_name, $species_tree_name );
    return $treerec->get_gene_tree_file($json);
}

##########################################################################
# Usage      : $results_ref = get_species_tree_data( $treerec,
#                  $species_tree_name, $family_name );
#
# Purpose    : Gets the species tree data for the given species tree name
#              and, optionally, for the given gene family name.
#
# Returns    : A reference to the gene tree data.
#
# Parameters : $treerec           - an instance of IPlant::TreeRec.
#              $species_tree_name - the name of the species tree.
#              $family_name       - the gene family name.
#
# Throws     : IPlant::TreeRec::GeneFamilyNotFoundException
#              IPlant::TreeRec::TreeNotFoundException
#              IPlant::TreeRec::ReconciliationNotFoundException
#              IPlant::TreeRec::IllegalArgumentException
sub _get_species_tree_data {
    my ( $treerec, $species_tree_name, $family_name ) = @_;
    my $json = build_tree_args( $family_name, $species_tree_name );
    return $treerec->get_species_tree_data($json);
}

##########################################################################
# Usage      : $results_ref = get_gene_tree_file( $treerec,
#                  $species_tree_name, $family_name );
#
# Purpose    : Gets the species tree file information for the given
#              species tree name and, optionally, for the given species
#              tree name.
#
# Returns    : A reference to the gene tree data.
#
# Parameters : $treerec           - an instance of IPlant::TreeRec.
#              $family_name       - the gene family name.
#              $species_tree_name - the name of the species tree.
#
# Throws     : IPlant::TreeRec::GeneFamilyNotFoundException
#              IPlant::TreeRec::TreeNotFoundException
#              IPlant::TreeRec::ReconciliationNotFoundException
#              IPlant::TreeRec::IllegalArgumentException
sub _get_species_tree_file {
    my ( $treerec, $species_tree_name, $family_name ) = @_;
    my $json = build_tree_args( $family_name, $species_tree_name );
    return $treerec->get_species_tree_file($json);
}

##########################################################################
# Usage      : $json = build_tree_args( $family_name,
#                  $species_tree_name );
#
# Purpose    : Builds the JSON string to be passed to the methods used
#              to get tree data and files.
#
# Returns    : The JSON string.
#
# Parameters : $family_name       - the name of the gene family.
#              $species_tree_name - the name of the species tree.
#
# Throws     : No exceptions.
sub build_tree_args {
    my ( $family_name, $reconciliation_set_id ) = @_;

    # Build the arguments JSON.
    my $args_ref = { familyName => $family_name };
    if ( defined $reconciliation_set_id ) {
        $args_ref->{reconciliationSetId} = $reconciliation_set_id;
    }
    my $json = JSON->new()->encode($args_ref);

    return $json;
}

__END__

=head1 NAME

UNKNOWN


=head1 VERSION

This documentation refers to UNKNOWN version NA


=head1 SYNOPSIS

	use 


=head1 SUBROUTINES/METHODS


=head1 LICENSE & COPYRIGHT

Copyright (c) 2011, The Arizona Board of Regents on behalf of The University of Arizona

All rights reserved.

Developed by: iPlant Collaborative at BIO5 at The University of Arizona http://www.iplantcollaborative.org

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

 * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 * Neither the name of the iPlant Collaborative, BIO5, The University of Arizona nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

=cut