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Revision 1.4 - (download) (as text) (annotate)
Mon Jan 29 18:59:08 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 1.3: +1 -1 lines
debugged version of bring_tree_up_to_ali

use FIG;
use tree_utilities;

$usage = "usage: evaluate_quality_of_trees [-t TreeFile] [-a Alpha] Alignment Trees";

my $against_treeF = undef;
my $alpha         = undef;
while ($ARGV[0] =~ /^-/)
{
    $_ = shift @ARGV;
    if ($_ =~ s/^-t//)    { $against_treeF = ($_ || shift @ARGV) }
    if ($_ =~ s/^-a//)    { $alpha         = ($_ || shift @ARGV) }
    else                  { die "Bad Flag: $_" }
}

my $dir = "$FIG_Config::temp/eval_qual.$$";
mkdir($dir,0777) || die "could not make $dir";

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

$/ = ";\n";
open(TREES,"<$treeF") || die "could not open $treeF";
while (defined($_ = <TREES>))
{
    if ($_ =~ /;/s)
    {
	$_ = &fix_expon($_);
	push(@trees,$_);
    }
}
close(TREES);
$/ = "\n";

my $tree;
foreach $tree (@trees)
{
    &eval_a_tree($tree,$aliF,$dir,$alpha,$against_treeF);
}
system "rm -rf $dir";

sub eval_a_tree {
    my($tree,$aliF,$dir,$alpha,$against_treeF) = @_;

    my $alpha_parm = $alpha ? "-a $alpha" : "";
    my $treeP = &tree_utilities::parse_newick_tree($tree);
    my $tips    = &tree_utilities::tips_of_tree($treeP);
    my %tips = map { $_ => 1 } @$tips;

    my $tmp_aliF = "$dir/ali.fasta";
    open(OUT,">$tmp_aliF") || die "could not open $tmp_aliF";
    open(IN,"<$aliF") || die "could not open $aliF";
    $/ = "\n>";
    while (defined($_ = <IN>))
    {
	chomp;
	if (($_ =~ /^>?(\S+)[^\n]*\n(\S.*\S)/s) && $tips{$1})
	{
	    print OUT ">$1\n$2\n";
	}
    }
    close(IN);
    close(OUT);
    $/ = "\n";

    system("/bin/rm -f $dir/in* $dir/out*");
    &FIG::run("echo Y > $dir/Y");
    if (! $against_treeF)
    {
	system "make_neigh_joining_tree $alpha_parm $tmp_aliF > $dir/against.outtree";
    }
    else
    {
	system "cp $against_treeF $dir/against.outtree";
    }
    system "echo 2 | cat - $dir/against.outtree > $dir/intree";
    open(TREES,">>$dir/intree") || die "could not open $dir/intree";
    print TREES $tree;
    close(TREES);

    &FIG::run("fasta_to_phylip < $tmp_aliF > $dir/infile");
    &FIG::run("/bin/rm -f $dir/out*");

    open(UY,">$dir/UY") || die "could not open UY";
    if ($alpha)
    {
	print UY "U\nR\nY\n",1 / sqrt($alpha),"\n5\n13\n";
    }
    else
    {
	print UY "U\nY\n";
    }
    close(UY);

    &FIG::run("cd $dir; proml < UY > /dev/null");
    my @tmp = `cat $dir/outfile`;
    my $i;
    for ($i=0; ($i < @tmp) && ($tmp[$i] !~ /^Kishino/); $i++) {}
    if ($i < @tmp)
    {
	print "First tree is neighbor-joining; second is one being tested\n";
	while ($i < @tmp)
	{
	    print $tmp[$i];
	    $i++;
	}
    }
    else
    {
	print STDERR "something went wrong\n",join("",@tmp);
    }
    print "================\n\n";
    &FIG::run("rm $dir/in* $dir/out*");
}
	      
sub fix_expon {
    my($tree) = @_;

    if ($tree =~ /^(.*:\s*)(\d*)\.(\d+)e-(\d+)(.*)/s)
    {
	my($before,$bad1,$bad2,$bad3,$after) = ($1,$2,$3,$4,$5);
	return &fix_expon($before) . &conv($bad1,$bad2,$bad3) . &fix_expon($after);
    }
    else
    {
	return $tree;
    }
}

sub conv {
    my($bad1,$bad2,$bad3) = @_;

    return "0." . ("0" x ($bad3 - length($bad1))) . $bad1 . $bad2;
}

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