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Revision 1.1 - (download) (as text) (annotate)
Thu Feb 1 20:49:10 2007 UTC (13 years ago) by golsen
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
Replace make_proml_tree with entirely new version.  Move the former
version to make_proml_tree_0.

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

use FIG;
use tree_utilities;
use Sys::Hostname;

$usage = "usage: make_proml_tree [-a Alpha] Alignment Outfile OutTree";

my $host = hostname;
my $dir = "$FIG_Config::temp/proml.$host.$$";
mkdir($dir,0777) || die "could not make $dir";
 
my $alpha = undef;
while ($ARGV[0] =~ /^-/)
{
    $_ = shift @ARGV;
    if ($_ =~ s/^-a//) { $alpha = ($_ || shift @ARGV) }
    else               { die "Bad Flag: $_" }
}


(
 ($aliF    = shift @ARGV) &&
 ($outF    = shift @ARGV) &&
 ($treeF   = shift @ARGV)
)
    || die $usage;

&FIG::run("fasta_to_phylip < $aliF > $dir/infile");
open(PARMS,">$dir/parms") || die "could not open $dir/parms";
$val = (int(rand() * 500000000) * 2) + 1;
print PARMS "J\n$val\n1\n";
if    ($alpha) { print PARMS "R\nY\n",1 / sqrt($alpha),"\n5\n"; }
else           { print PARMS "Y\n"; }
close(PARMS);
system "cd $dir; proml < parms > log";
system "mv $dir/outfile $outF; mv $dir/outtree $treeF; rm -r $dir";
system "/bin/rm -r $dir";

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