[Bio] / FortyEightMeta / mg_norm_silva.pl Repository:
ViewVC logotype

View of /FortyEightMeta/mg_norm_silva.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (as text) (annotate)
Fri May 30 23:23:51 2008 UTC (11 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, mgrast_rel_2008_0806, mgrast_dev_10262011, mgrast_dev_02212011, mgrast_rel_2008_0923, mgrast_release_3_0, mgrast_dev_03252011, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, 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, mgrast_dev_04012011, mgrast_rel_2008_0919, mgrast_rel_2008_1110, myrast_33, mgrast_rel_2008_0917, mgrast_dev_04052011, mgrast_dev_02222011, HEAD
Development checkin of new metagenomics RAST pipeline.

#
# normalize silva taxonomy data.
#

while (<>)
{
    chomp;
    my @cols = split(/\t/);

    my($id, $species, $tax);
    if ($cols[0] =~ /^\s*(\S+)\s+\|\s+(.*)\s*$/)
    {
	$id = $1;
	$species = $2
    }
    else
    {
	next;
    }

    my @tax = grep { $_ ne '' } split(/\s*;\s*/, $cols[1]);
    print join("\t", $id, @tax, $species), "\n";
}
       

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3