[Bio] / FigKernelScripts / svr_is_hypo.pl Repository:
ViewVC logotype

View of /FigKernelScripts/svr_is_hypo.pl

Parent Directory Parent Directory | Revision Log Revision Log

Revision 1.3 - (download) (as text) (annotate)
Thu Apr 7 22:11:18 2011 UTC (8 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_release_3_0_4, mgrast_dev_06072011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, rast_rel_2014_0729, mgrast_dev_05262011, mgrast_release_3_1_2, mgrast_release_3_1_1, rast_rel_2011_0928, mgrast_dev_04132011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_10262011, mgrast_dev_04082011, mgrast_release_3_1_0, HEAD
Changes since 1.2: +14 -2 lines
minor fixes

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

# This is a SAS Component

=head1 svr_is_hypo [-c N] [-v]

Keep just hypotheticals



    svr_all_features 3702.1 peg | svr_is_hypo

would produce a 1-column table containing the hypotheticals in 3702.1

Normally, a stream of feature IDs (PEGs) is used as input.  If the things you send
through do not look like PEGs, then they are treated as functional roles.


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 .  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.

=item -v [keep only non-hypotheticals]


=head2 Output Format

This is a filter producing a subset of the input lines.


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

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

my $column;
my $v;
my $rc  = GetOptions('c=i' => \$column,
		     'v'   => \$v);
if (! $rc) { print STDERR $usage; exit }

my @lines = map { chomp; [split(/\t/,$_)] } <STDIN>;
(@lines > 0) || exit;
if (! $column)  { $column = @{$lines[0]} }
my @fids = grep { $_ =~ /^fig\|/ } map { $_->[$column-1] } @lines;

my $functions = $sapObject->ids_to_functions(-ids => \@fids);
foreach $_ (@lines)
    my $thing = $_->[$column-1];
    my $func;
    if ($thing =~ /^fig\|/)
	$func = $functions->{$thing};
	$func = $thing;
    my $hypo = &SeedUtils::hypo($func);
    if (((! $v) && $hypo) || ($v && (! $hypo)))
	print join("\t",@$_),"\n";

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3