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Revision 1.1 - (download) (as text) (annotate)
Thu Oct 21 13:02:28 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_dev_06072011, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2011_0119, 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_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011
Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes".

use strict;
use SeedEnv;

# This is a SAS Component

=head1 svr_roles_to_subsys

Extend a set of roles to include the subsystems and category data

=head2 Introduction


    svr_roles_to_subsys -all < table.with.roles.as.last.column > extended.table
        extend to all subsystems, including cluster-based (defaults to just usable, non-cluster-based)

    svr_roles_to_subsys -c 2 -aux < table.with.roles.as.last.column > extended.table
        extend from roles in column 2 to usable, non-cluster-based subsys including thoise in which 
        the role is auxiliary

=head2 Command-Line Arguments

The program is invoked using

    svr_role_to_subsys [-all] [-aux] [-c Column] < table.with.role.column > with.3.more.columns

=over 4

=item -all

Use all subsystems, including experimental and cluster-based [default is only usable, non-cluster-based]

=item -aux 

Include subsystemns in which the role is auxiliary [default is to ignore auxiliary roles]

=item -c=Column

Specifies the column in the input table that is believed to contain the role.


=head2 Output

A table with 2 added columnns (subsystem, comma-delimited list of categories).
Lines in the incoming table that do not match are written to STDERR.


use Getopt::Long;
my $usage = "svr_roles_to_subsys [-all] [-aux] [-c Column] < table.with.roles > extended.table 2> nonconnecting.rows\n";

my $all = 0;
my $aux = 0;
my $column;
my $url = '';

my $rc = GetOptions( "all" => \$all,
                     "aux"   => \$aux,
                     "c=i" => \$column,
                     "url=s" => \$url

$rc or print STDERR $usage and exit;

# Get the server object.
my $sapServer = SAPserver->new(url => $url);
# We'll use this to cache subsystem classifications.
my %subClasses;
# Compute the auxiliary parameters.
my %auxParms;
if ($aux) {
    $auxParms{-aux} = 1
if ($all) {
    $auxParms{-usable} = 0
} else {
    $auxParms{-exclude} = 'cluster-based';
# The main loop processes chunks of input, 1000 lines at a time.
while (my @tuples = ScriptThing::GetBatch(\*STDIN, undef, $column)) {
    # Ask the server for the subsystems.
    my $roleHash = $sapServer->subsystems_for_role(-ids => [map { $_->[0] } @tuples],
    # Collect the new subsystems we've found this time.
    my @subs;
    for my $role (keys %$roleHash) {
        my $subList = $roleHash->{$role};
        for my $sub (@$subList) {
            if (! exists $subClasses{$sub}) {
                push @subs, $sub;
    # Get the classifications for these subsystems.
    my $subHash = $sapServer->classification_of(-ids => \@subs);
    # Put them in the classification hash.
    for my $sub (@subs) {
        $subClasses{$sub} = join(", ", @{$subHash->{$sub}});
    # Output the results for these roles.
    for my $tuple (@tuples) {
        # Get this line and the relevant role.
        my ($role, $line) = @$tuple;
        # Get this role's subsystems.
        for my $sub (@{$roleHash->{$role}}) {
            # Output the line with the subsystem and classification appended.
            print join("\t", $line, $sub, $subClasses{$sub}) . "\n";

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