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Revision 1.2 - (download) (as text) (annotate)
Thu Mar 10 19:06:42 2011 UTC (8 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2014_0729, mgrast_dev_03252011, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_10262011, HEAD
Changes since 1.1: +33 -11 lines
minor fixes

use strict;

use Getopt::Long;
use ScriptThing;
use SAPserver;

# This is a SAS Component

=head1 svr_neighboring_reactions

Takes as input a table containing reaction IDs and 
adds 2 columns giving the distance and the connected reaction.

Example: svr_all_reactions | svr_neighboring_reactions -d 2 > table.with.neighboring.reactions

would produce a 3-column table: [reactionID1,Distance,ReactionID2]

         svr_neighboring_reactions -r rxn09225

would produce a 3-column table in which each line represents a reaction
connected (immediately connected, since -d defaults to 1) to rxn09225.



=head2 Command-Line Options

=over 4

=item -c Column

This is used only if the column containing reaction IDs is not the last.

=item -d MaxDist [default=1]

Gives the maximum distance.  The computation becomes extremely expensive as this value
goes up.

=item -r Reaction

Gives a single reaction, rather than taking reactions from an input file.


=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with two extra columns (distance and connected reaction).


use SeedUtils;
use SAPserver;
my $sapObject = SAPserver->new();
use Getopt::Long;

my $usage = "usage: svr_neighboring_reactions [-c column] [-d MaxDistance] [-r reaction]";

my $column;
my $max_dist = 1;
my $reaction;
my $rc  = GetOptions('c=i' => \$column,
		     'r=s' => \$reaction,
                     'd=i' => \$max_dist
if (! $rc) { print STDERR $usage; exit }

if (! $reaction)
    while (my @lines = ScriptThing::GetBatch(\*STDIN, 10, $column)) {
	my $reactionsH = $sapObject->reaction_neighbors( -ids => [map { $_->[0] } @lines],
							 -depth => $max_dist );
	for my $line (@lines) {
	    my ($rxn, $text) = @$line;
	    my $neighborH = $reactionsH->{$rxn};
	    for my $neighbor (sort keys %$neighborH) {
		print "$text\t$neighbor\t$neighborH->{$neighbor}\n";
    my $reactionsH = $sapObject->reaction_neighbors( -ids => [$reaction], -depth => $max_dist );
    my $neighborH = $reactionsH->{$reaction};
    for my $neighbor (sort keys %$neighborH) {
	print "$reaction\t$neighbor\t$neighborH->{$neighbor}\n";

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