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lib/LiteratureBasedDiscovery/Discovery.pm  view on Meta::CPAN

    open IN, $fileName or die ("unable to open file: $fileName\n");
    my %matrix = ();
    my ($cui1,$cui2,$val);
    while (my $line = <IN>) {
	chomp $line;
	($cui1,$cui2,$val) = split(/\t/,$line);
	
	if (!exists $matrix{$cui1}) {
	    my %hash = ();
	    $matrix{$cui1} = \%hash;
	}
	$matrix{$cui1}{$cui2} = $val;
    }
    close IN;
    return \%matrix;
}

# outputs the matrix to the output file in sparse matrix format, which
# is a file containing rowKey\tcolKey\tvalue
# input:  $outFile - a string specifying the output file
#         $matrixRef - a ref to the sparse matrix containing the data
# output: nothing, but the matrix is output to file
sub outputMatrixToFile {
    my $outFile = shift;
    my $matrixRef = shift;
    
    #open the output file and output fhe matrx
    open OUT, ">$outFile" or die ("Error opening matrix output file: $outFile\n");
    my $rowRef;
    foreach my $rowKey (keys %{$matrixRef}) {
	$rowRef = ${$matrixRef}{$rowKey};
	foreach my $colKey (keys %{$rowRef}) {
	    print OUT "$rowKey\t$colKey\t${$rowRef}{$colKey}\n";
	}
    }
}


#Note: Table to sparse is no longer used, but could be useful in the future
=comment
#  retreive a table from mysql and convert it to a sparse matrix (a hash of 
#     hashes)
#  input : $tableName <- the name of the table to output
#          #cuiFinder <- an instance of UMLS::Interface::CuiFinder
#  output: a hash ref to the sparse matrix (${$hash{$index1}}{$index2} = value)
sub tableToSparseMatrix {
    my $tableName = shift;
    my $cuiFinder = shift;

    # check tableName
    #TODO check that the table exists in the database
    # or die "Error: table does not exist: $tableName\n";

    #  set up database
    my $db = $cuiFinder->_getDB(); 
    
    # retreive the table as a nested hash where keys are CUI1, 
    # then CUI2, value is N11
     my @keyFields = ('cui_1', 'cui_2');
     my $matrixRef = $db->selectall_hashref(
	"select * from $tableName", \@keyFields);

    # set values of the loaded table to n_11
    # ...default is hash of hash of hash
    foreach my $key1(keys %{$matrixRef}) {
	foreach my $key2(keys %{${$matrixRef}{$key1}}) {
	    ${${$matrixRef}{$key1}}{$key2} = ${${${$matrixRef}{$key1}}{$key2}}{'n_11'};
	}
    }
    return $matrixRef;
}
=cut

1;