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1 : overbeek 1.1 # -*- perl -*-
2 :     #
3 :     # Copyright (c) 2003-2008 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 :     #
8 :     # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 :     # Public License.
11 :     #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 :     #
18 :    
19 :    
20 :     use strict;
21 :     use Data::Dumper;
22 :    
23 :     use FIG;
24 :     use FIG_CGI;
25 :    
26 :     use URI::Escape; # uri_escape
27 :     use HTML;
28 :     my $fig = new FIG;
29 :     use CGI;
30 :     my $cgi = new CGI;
31 :    
32 :     if (0)
33 :     {
34 :     print $cgi->header;
35 :     my @params = $cgi->param;
36 :     print "<pre>\n";
37 :     foreach $_ (@params)
38 :     {
39 :     print "$_\t:",join(",",$cgi->param($_)),":\n";
40 :     }
41 :     exit;
42 :     }
43 :    
44 : disz 1.2 my $subsys = "$FIG_Config::data/Subsystems";
45 :     #my $subsys = "/vol/core-seed/FIGdisk/FIG/Data/Subsystems";
46 : overbeek 1.1
47 :     my $html = [];
48 :     unshift @$html, "<TITLE>Subsystem-based compare-regions</TITLE>\n";
49 :     my $ss = $cgi->param('ss');
50 :     my $abbr = $cgi->param('abbr');
51 :    
52 :     if ((! $ss) || (! $abbr))
53 :     {
54 :     push(@$html,"<h1> ERROR: You need to use ss= and abbr= parameters</h1>");
55 :     &HTML::show_page($cgi,$html);
56 :     exit;
57 :     }
58 :     if (! -s "$subsys/$ss/spreadsheet")
59 :     {
60 :     push(@$html,"<h1> ERROR: No such subsystemp in coreSEED ($subsys)</h1>");
61 :     &HTML::show_page($cgi,$html);
62 :     exit;
63 :     }
64 : olson 1.3 my @pegs = &pegs_in_spreadsheet("$subsys/$ss",$abbr,$fig);
65 : overbeek 1.1
66 :     if (@pegs == 0)
67 :     {
68 :     push(@$html,"<h1> ERROR: No pegs in $abbr of $subsys</h1>");
69 :     &HTML::show_page($cgi,$html);
70 :     exit;
71 :     }
72 :    
73 :     my $number_pegs = $cgi->param('n');
74 :     if (! $number_pegs) { $number_pegs = 10 }
75 :     while (@pegs > 0)
76 :     {
77 :     my $sz = (@pegs > $number_pegs) ? $number_pegs : @pegs;
78 :     my @batch = splice(@pegs,0,$sz);
79 : olson 1.3 my @bpegs = map { $_->[0] } @batch;
80 :     my $start_href = &link(\@bpegs);
81 :     my $start_link = "<a target=_blank href=$start_href>$batch[0]->[0] $batch[0]->[2]</a><br>\n";
82 : overbeek 1.1 push(@$html,"<br><br>",$start_link,"<br>\n");
83 : olson 1.3
84 :     push(@$html, "<a target=_blank href='$FIG_Config::cgi_url/seedviewer.cgi?feature=$_->[0]'>$_->[0]</a><br>\n") foreach @batch;
85 :    
86 : overbeek 1.1 }
87 :    
88 :     &HTML::show_page($cgi,$html);
89 :    
90 :     sub link {
91 :     my($pegs) = @_;
92 :    
93 :     my $features = join('&feature=',@$pegs);
94 : disz 1.2 return "$FIG_Config::cgi_url/seedviewer.cgi?page=Regions&feature=" . $features;
95 :     #return "http://core.theseed.org/FIG/seedviewer.cgi?page=Regions&feature=" . $features;
96 : overbeek 1.1 }
97 :    
98 :     sub pegs_in_spreadsheet {
99 : olson 1.3 my($ssF,$abbr,$fig) = @_;
100 : overbeek 1.1
101 :     my $spreadsheet = join("",`cat $ssF/spreadsheet`);
102 :     my($hdrs,undef,$genomes) = split(/\n\/\/\n/,$spreadsheet);
103 :     my @hdrs = map { ($_ =~ /^(\S+)/) ? $1 : () } split(/\n/,$hdrs);
104 :     my $i;
105 :     for ($i=0; ($i < @hdrs) && ($hdrs[$i] ne $abbr); $i++) {}
106 :     my @pegs;
107 :     foreach $_ (split(/\n/,$genomes))
108 :     {
109 :     my @rows = split(/\t/,$_);
110 :     my $g = shift @rows;
111 :     shift @rows; # dump variant code
112 :     push(@pegs,map { "fig|$g.peg.$_" } split(/,/,$rows[$i]));
113 :     }
114 : olson 1.3 @pegs = grep { $fig->is_real_feature($_) } @pegs;
115 :     my @tuples = map { [$_,$fig->taxonomy_of(&SeedUtils::genome_of($_)),$fig->genus_species(&SeedUtils::genome_of($_))] } @pegs;
116 :     @tuples = sort { $a->[1] cmp $b->[1] } @tuples;
117 :     #print STDERR Dumper(\@tuples);
118 :     #return map { $_->[0] } @tuples;
119 :     return @tuples;
120 : overbeek 1.1 }

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