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Revision 1.1 - (download) (annotate)
Mon Dec 18 23:53:03 2006 UTC (13 years, 2 months ago) by hwang
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
given a tyra peg/ it finds the gene neighborhood of that peg

use CGI;

my $cgi = new CGI;
print $cgi->header();
my $id = $cgi->param("seq");

open(SEQFILE, "Html/group_name_desc_seq.html") or print "Can't find sequence file";
my @seqfile = <SEQFILE>;
my $pinned_string;

#Store hash of where it is store at
my %name_to_group = ();

foreach(@seqfile) {
    my($group, $name, $desc, $theseq) = split(/\t/,$_);
    my($peg,$res) = split(/_/,$desc);
    $peg=~ s/\s+//;

    if ($desc =~ /fig\|/) {
	$name_to_group {$name} = "$group\t$peg";
	#print "$name $peg<p>";
    else {
	$name_to_group {$name} = $group;


my $query_group_peg = $name_to_group{$id};
#print "What is the peg here $query_group_peg<-- what is the id $id\n";
my($query_group, $query_peg) = split(/\t/,$query_group_peg);

if($query_peg eq "") {
    print "$id does not have a peg. Cannot use chromosomal cluster tool\n";

foreach(@seqfile) {
    my($group, $name, $desc, $theseq) = split(/\t/,$_);
    next unless ($desc =~ /fig\|/);
    next if ($id eq name);
    next unless ($query_group eq $group);

    my ($peg, $rest) = split(/_/,$desc);
    $peg=~ s/\s+//;
    $pinned_string .= "pinned_to=$peg&";

$parms = "prot=$query_peg&$pinned_string&sim_cutoff=1.0e-8";  

#print "<p>the query is $parms<p>"; 
$ENV{'QUERY_STRING'} = $parms;                                                                  

@out = `./chromosomal_clusters.cgi 2> /dev/null`;                                               
for ($i=$#out; ($i >= 0) && ($out[$i] !~ /^Content-Type/); $i--) {}                             
while ($i < @out)                                                                               
    print $out[$i];                                                                            

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