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Revision 1.2 - (download) (as text) (annotate)
Sat Apr 11 22:23:45 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, 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, rast_rel_2014_0729, 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, HEAD
Changes since 1.1: +3 -3 lines
fix order of arguments

use Data::Dumper;
use Contigs;
use strict;
use compare_coding;

my $usage = "usage: mark_picked_genes GenomesFile ScoredAlignments Picked HTML";

my($genomes,$aliD,$htmlD,$pickedD);

(
 ($genomes    = shift @ARGV) && open(GEN,"<$genomes") &&
 ($aliD       = shift @ARGV) && opendir(ALIS,$aliD) &&
 ($pickedD    = shift @ARGV) && (-d $pickedD) &&
 ($htmlD      = shift @ARGV)
)
    || die $usage;


my @genomes = map { $_ =~ /^(\S+)/; $1 } <GEN>;
close(GEN);

my %orig_ids;
foreach my $genome (@genomes)
{
    open(PICKED,"<$pickedD/$genome") || die "could not open $pickedD/$genome";
    while (defined($_ = <PICKED>))
    {
	chomp;
	my($type,$loc,$sc,%extra) = split(/\t/,$_);
	if ($extra{orig_id})
	{
	    $orig_ids{$extra{orig_id}} = $loc;
	}
    }
    close(PICKED);
}

my @alis = grep { $_ !~ /^\./ } readdir(ALIS);
closedir(ALIS);

(-d $htmlD) || mkdir($htmlD,0777) || die "could not make $htmlD";

foreach my $file (@alis)
{
    open(IN,"<$aliD/$file") || die "could not open $aliD/$file";
    $file =~ s/\.[^\.]*$//;

    my @ali = ();
    while (defined($_ = <IN>))
    {
	chomp;
	push(@ali,[split(/\t/,$_)]);
    }
    close(IN);
    my $init_scores = pop @ali; 
    my $scores      = pop @ali;
    my %locs = map { $_->[0] => $_->[1] } @ali;
    my $opts = { loc1 => \%orig_ids };
    my $html = &compare_coding::display_scored_dna(\@ali,\%locs,$scores,$init_scores,$opts);
    open(HTML,">$htmlD/$file.html") || die "$htmlD/$file.html";
    print HTML $html,"\n";
    close(HTML);
}


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