[Bio] / FigKernelScripts / p3-generate-clusters.pl Repository:
ViewVC logotype

View of /FigKernelScripts/p3-generate-clusters.pl

Parent Directory Parent Directory | Revision Log Revision Log

Revision 1.4 - (download) (as text) (annotate)
Fri Aug 11 01:13:02 2017 UTC (2 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.3: +1 -1 lines
Changes copied from SEEDtk project.

=head1 Generate Clusters From Pairs Using Transitive Closure

    p3-generate-clusters.pl [options] col1 col2

This script reads in a tab-delimited file representing pairs of objects and generates a transitive closure to
create clusters.

The clusters will be output one per line, with a specified delimiter between elements. The default delimiter is C<::>,
but you can specify a tab, a space, or any character sequence that doesn't appear in any element of the pair.

=head2 Parameters

The positional parameters are the names or 1-based indices of the two columns containing the object names. So, an invocation of

    p3-generate_clusters 1 2

would indicate the first two columns contain the paired object names. An invocation of

    p3-generate-clusters role1 role2

would process the output from L<p3-generate-close-roles.pl>.

The standard input can be overriddn using the options in L<P3Utils/ih_options>. Use the options in L<P3Utils/delim_options> to
specify the delimiter.

Additional command-line options are as follows.

=over 4

=item title

Title to give to the output column. The default is <cluster>.



use strict;
use P3Utils;

# Get the command-line options.
my $opt = P3Utils::script_opts('col1 col2', P3Utils::ih_options(), P3Utils::delim_options(),
        ['title|t=s', 'output column title', { default => 'cluster'} ]
# Verify the positional parameters.
my ($col1, $col2) = @ARGV;
if (! $col1 || ! $col2) {
    die "Two column names/indices are required.";
# Compute the delimiter.
my $delim = P3Utils::delim($opt);
# Open the input file.
my $ih = P3Utils::ih($opt);
# Find the object name columns.
my ($headers, $cols) = P3Utils::find_headers($ih, pair => $col1, $col2);
# This hash will map each object name to its group number.
my %objectMap;
# This list contains the groups.
my @groupList;
# Loop through the input.
while (! eof $ih) {
    # Get the object names for this row.
    my ($obj1, $obj2) = P3Utils::get_cols($ih, $cols);
    # Make sure they are in the same group.
    my $group1 = $objectMap{$obj1};
    my $group2 = $objectMap{$obj2};
    if (defined $group1 && ! defined $group2) {
        # Object 2 is new, belongs in group 1.
        $objectMap{$obj2} = $group1;
        push @{$groupList[$group1]}, $obj2;
    } elsif (! defined $group1 && defined $group2) {
        # Object 1 is new, belongs in gorup 2.
        $objectMap{$obj1} = $group2;
        push @{$groupList[$group2]}, $obj1;
    } elsif (! defined $group1 && ! defined $group2) {
        # Both are new. Create a new group. Note we have special code for the case where the same
        # object has occurred twice.
        $group1 = scalar @groupList;
        my @newGroup = ($obj1);
        if ($obj2 ne $obj1) {
            push @newGroup, $obj2;
        push @groupList, \@newGroup;
        $objectMap{$obj1} = $group1;
        $objectMap{$obj2} = $group1;
    } elsif ($group1 != $group2) {
        # Both are old. Merge group2 into group1.
        my $group2Objects = $groupList[$group2];
        for my $obj (@$group2Objects) {
            $objectMap{$obj} = $group1;
        push @{$groupList[$group1]}, @$group2Objects;
        $groupList[$group2] = [];
# Delete the empty groups and sort from largest to smallest.
my @sorted = sort { scalar(@$b) <=> scalar(@$a) } grep { scalar(@$_) } @groupList;
# Output the groups.
my $title = $opt->title;
P3Utils::print_cols([$title . "_id", 'size', $title]);
my $cluster_id = 1;
for my $group (@sorted) {
    P3Utils::print_cols([$cluster_id, scalar @$group, $group], opt => $opt);

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3