[Bio] / FigKernelScripts / p3-set-to-relation.pl Repository:
ViewVC logotype

View of /FigKernelScripts/p3-set-to-relation.pl

Parent Directory Parent Directory | Revision Log Revision Log

Revision 1.3 - (download) (as text) (annotate)
Fri Aug 11 01:13:02 2017 UTC (2 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.2: +11 -6 lines
Changes copied from SEEDtk project.

=head1 Convert a Table of Sets to a Relation Table

    p3-set-to-relation.pl [options]

This script will look at an input file that has sets in a single column. Each set is represented by a list of items
separated by a delimiter (default C<::>). Each set is given a number, and the output file puts
one set element on each line along with its set number, thus improving readability.

=head2 Parameters

There are no positional parameters.

The standard input can be overriddn using the options in L<P3Utils/ih_options>.

Additional command-line options are those given in L<P3Utils/col_options> which specifies the input
column, L<P3Utils/delim_options> which specifies the delimiter between set items, and the following.

=over 4

=item idCol

The index (1-based) or name of the column containing the set ID. If omitted, the set IDs are generated internally.



use strict;
use P3DataAPI;
use P3Utils;

# Get the command-line options.
my $opt = P3Utils::script_opts('', P3Utils::ih_options(), P3Utils::col_options(),
        ['idCol|idcol|id=s', 'index (1-based) or name of cluster ID column']
# Open the input file.
my $ih = P3Utils::ih($opt);
# Read the incoming headers.
my ($outHeaders, $keyCol) = P3Utils::process_headers($ih, $opt);
# Find the ID column.
my $idCol = $opt->idcol;
if (defined $idCol) {
    $idCol = P3Utils::find_column($idCol, $outHeaders);
# Compute the delimiter pattern.
my $delim = P3Utils::undelim($opt);
# Write the output headers.
P3Utils::print_cols(['id', 'element']);
# Initialize the ID.
my $id = 0;
# Loop through the input.
while (! eof $ih) {
    my $couplets = P3Utils::get_couplets($ih, $keyCol, $opt);
    for my $couplet (@$couplets) {
        my $cluster = $couplet->[0];
        # Compute this cluster's ID.
        if (defined $idCol) {
            $id = $couplet->[1][$idCol];
        } else {
        my @items = split $delim, $cluster;
        for my $item (sort @items) {
            P3Utils::print_cols([$id, $item]);

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3