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

View of /FigKernelScripts/reps_and_close.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (download) (as text) (annotate)
Sat May 12 21:22:23 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, 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, mgrast_dev_02212011, 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, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +1 -0 lines
add make_trimmed_alignment_from_ids

########################################################################

use strict;
use gjoseqlib;
use representative_sequences;

my $usage = "usage: reps_and_close [-t TargetN] [-m MaxIden] Representatives Sets < Seqs";

my $targetN  = 50;
my $max_iden = 0.9;

while ( $ARGV[0] =~ /^-/ )
{
    $_ = shift;
    if    ( s/^-t// ) { $targetN      = $_ || shift }
    elsif ( s/^-m// ) { $max_iden     = $_ || shift }
    else
    {
        usage( "Bad command flag '$_'\n" );
    }
}

my($repfile,$setfile);
(($repfile = shift @ARGV)  && open(REPS,">$repfile"))
    || die $usage;

(($setfile = shift @ARGV)  && open(SETS,">$setfile"))
    || die $usage;

my $seqs = &gjoseqlib::read_fasta();
my($reps,$sets) = &representative_sequences::n_rep_seqs({ seqs     => $seqs, 
							  by_size  => 1,
							  max_rep  => $targetN,
							  max_iden => $max_iden 
							});
foreach my $tuple (@$reps)
{
    &gjoseqlib::print_seq_as_fasta(\*REPS,@$tuple);
}
close(REPS);

foreach my $id (keys(%$sets))
{
    my $x = $sets->{$id};
    print SETS "$id\t",join(",",@$x),"\n";
}

sub usage
{
    print STDERR join( "\n", @_, $usage );
    exit;
}



MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3