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Revision 1.11 - (download) (as text) (annotate)
Tue May 31 20:39:41 2011 UTC (8 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, myrast_rel40, mgrast_dev_06072011, mgrast_release_3_1_1, mgrast_release_3_1_0, rast_rel_2011_0928, mgrast_dev_10262011
Changes since 1.10: +16 -13 lines
Converted to use "GetBatch" to flow-control the requests.

use strict;
use Data::Dumper;
use Carp;

#
# This is a SAS Component
#


=head1 svr_function_of

Get functions of protein-encoding genes

------

Example:

    svr_all_features 3702.1 peg | svr_function_of

would produce a 2-column table.  The first column would contain
PEG IDs for genes occurring in genome 3702.1, and the second
would contain the functions of those genes.

------

The standard input should be a tab-separated table (i.e., each line 
is a tab-separated set of fields).  Normally, the last field in each
line would contain the PEG for which functions are being requested.
If some other column contains the PEGs, use

    -c N

where N is the column (from 1) that contains the PEG in each case.

This is a pipe command. The input is taken from the standard input, and the
output is to the standard output.

=head2 Command-Line Options

=over 4

=item -c Column

This is used only if the column containing PEGs is not the last.

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with an extra column added (the function associated with the PEG).

=cut

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

my $usage = "usage: svr_function_of [-c column]";

my $column;
my $i = "-";
my $rc  = GetOptions('c=i' => \$column, 'i=s' => \$i);
if (! $rc) { print STDERR $usage; exit }
open my $ih, "<$i";
while (my @tuples = ScriptThing::GetBatch($ih, undef, $column)) {
    my @ids = map { $_->[0] } @tuples;
    my $functions = $sapObject->ids_to_functions(-ids => \@ids);
    for my $tuple (@tuples) {
        my ($id, $line) = @$tuple;
        my $function = $functions->{$id};
        if (! defined $function) {
            print STDERR "$id not found.\n";
        } else {
            print "$line\t$function\n";
        }
    }
}

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