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Revision 1.1 - (download) (as text) (annotate)
Fri Jun 12 16:03:03 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2009_0925, rast_rel_2010_0526, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, 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_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011
code for processing fabrics and population estimates

# DESCRIPTION OF check_consistency_of_sample.pl
# 
# You can use
# 
# 	perl pop_vec.pl < Sample > population.estimate
# 
# Sample can be a file in the 5-column format, or it can be a file
# of genus-species (in a 1-column format)

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

my($sample);
my $usage = "usage: perl [-k Column] pop_vec.pl <  sample";

my $N = 5;

while ( @ARGV && $ARGV[0] =~ s/^-// )
{
    $_ = shift;
    if ( s/^k// ) { $N    = $_ || shift; next }
    else
    {
        print STDERR "Bad flag '$_'\n", $usage;
        exit;
    }
}

my %gs;
while (defined($_ = <STDIN>))
{
    chomp; 
    my @flds = split(/\t/,$_);
    if ((@flds == 1) && $flds[0])
    {
	$gs{$flds[0]}++;
    }
    elsif (($N <= @flds) && $flds[$N-1])
    {
	$gs{$flds[$N-1]}++;
    }
    elsif ($flds[$N-1])
    {
	print STDERR "Invalid input: $_\n";
    }
}

foreach my $gsN (sort { $gs{$b} <=> $gs{$a} } keys(%gs))
{
    print join("\t",($gs{$gsN},$gsN)),"\n";
}


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