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Revision 1.2 - (download) (as text) (annotate)
Tue Oct 3 02:48:59 2006 UTC (13 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, 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, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +1 -1 lines
Fixed default trace level.

#!/usr/bin/perl -w

=head1 Feature Location Computer

This script adds feature locations to a data mining stream. The locations
are formatted as Sprout locations, consisting of the contig ID, the start
position, the direction, and the length. If a feature has multiple
locations, each one will produce a separate output line.

The currently-supported command-line options are as follows.

=over 4

=item keyColumn

Name or number of the column containing the feature ID.

=item user

Name suffix to be used for log files. If omitted, the PID is used.

=item trace

Numeric trace level. A higher trace level causes more messages to appear. The
default trace level is 2. Tracing will be directly to the standard output
as well as to a C<trace>I<User>C<.log> file in the FIG temporary directory,
where I<User> is the value of the B<user> option above.

=item sql

If specified, turns on tracing of SQL activity.

=item background

Save the standard and error output to files. The files will be created
in the FIG temporary directory and will be named C<err>I<User>C<.log> and
C<out>I<User>C<.log>, respectively, where I<User> is the value of the
B<user> option above.

=item h

Display this command's parameters and options.

=back

=cut

use strict;
use Tracer;
use FIG;
use Sprout;
use SFXlate;
use ERDB;

# Get the command-line options and parameters.
my ($options, @parameters) = StandardSetup([qw(Sprout ERDB SFXlate)],
                                           {
                                            keyColumn => ["Feature(id)", "column from which to take the feature ID"],
                                            trace => ["2-", "tracing level"],
                                           },
                                           "",
                                           @ARGV);
# Get the database.
my $sprout = SFXlate->new_sprout_only();
# Get the key column.
my $colName = $options->{keyColumn};
if (! $colName) {
    Confess("No source column name specified.");
} else {
    # Get the column headers.
    my $colhdrs = <STDIN>;
    # Verify that we have column headers.
    if (! defined($colhdrs)) {
        Confess("Nothing found in input.");
    } else {
        # Process the column headers.
        my @metaData = ERDB::ParseColumns($colhdrs);
        # Find the desired key column.
        my $sourceCol = ERDB::FindColumn($colhdrs, $colName);
        # Write out the new column headers.
        print join("\t", @metaData, 'Feature(location)') . "\n";
        # We will now loop through the input, appending feature locations to each
        # input line.
        while (my $line = <STDIN>) {
            # Pull the feature ID from the line.
            my @data = ERDB::ParseColumns($line);
            my $keyValue = $data[$sourceCol];
            # Get the feature's locations.
            my @locations = $sprout->FeatureLocation($keyValue);
            # Loop through the locations, producing output lines.
            for my $loc (@locations) {
                print join("\t", @data, $loc) . "\n";
            }
        }
    }
}

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