Parent Directory
| 
Revision Log
Revision 1.3.2.1 - (view) (download)
| 1 : | overbeek | 1.1 | #### start ##### |
| 2 : | olson | 1.3.2.1 | use InterfaceRoutines; |
| 3 : | |||
| 4 : | overbeek | 1.1 | |
| 5 : | use HTML; | ||
| 6 : | use strict; | ||
| 7 : | use CGI; | ||
| 8 : | my $cgi = new CGI; | ||
| 9 : | |||
| 10 : | olson | 1.3.2.1 | use FIG; |
| 11 : | my $sproutAvail = eval { | ||
| 12 : | require SproutFIG; | ||
| 13 : | require PageBuilder; | ||
| 14 : | }; | ||
| 15 : | |||
| 16 : | my($fig_or_sprout); | ||
| 17 : | my $is_sprout; | ||
| 18 : | my $html = []; | ||
| 19 : | |||
| 20 : | if ($cgi->param('SPROUT')) { | ||
| 21 : | $is_sprout = 1; | ||
| 22 : | $fig_or_sprout = new SproutFIG($FIG_Config::sproutDB, $FIG_Config::sproutData); | ||
| 23 : | unshift @$html, "<TITLE>The NMPDR Homologs in Clusters Page</TITLE>\n"; | ||
| 24 : | } else { | ||
| 25 : | $is_sprout = 0; | ||
| 26 : | $fig_or_sprout = new FIG; | ||
| 27 : | unshift @$html, "<TITLE>The SEED Homologs in Clusters Page</TITLE>\n"; | ||
| 28 : | } | ||
| 29 : | |||
| 30 : | overbeek | 1.1 | if (0) |
| 31 : | { | ||
| 32 : | my $VAR1; | ||
| 33 : | eval(join("",`cat /tmp/homologs_in_clusters_parms`)); | ||
| 34 : | $cgi = $VAR1; | ||
| 35 : | # print STDERR &Dumper($cgi); | ||
| 36 : | } | ||
| 37 : | |||
| 38 : | if (0) | ||
| 39 : | { | ||
| 40 : | print $cgi->header; | ||
| 41 : | my @params = $cgi->param; | ||
| 42 : | print "<pre>\n"; | ||
| 43 : | foreach $_ (@params) | ||
| 44 : | { | ||
| 45 : | print "$_\t:",join(",",$cgi->param($_)),":\n"; | ||
| 46 : | } | ||
| 47 : | |||
| 48 : | if (0) | ||
| 49 : | { | ||
| 50 : | if (open(TMP,">/tmp/homologs_in_clusters_parms")) | ||
| 51 : | { | ||
| 52 : | print TMP &Dumper($cgi); | ||
| 53 : | close(TMP); | ||
| 54 : | } | ||
| 55 : | } | ||
| 56 : | exit; | ||
| 57 : | } | ||
| 58 : | |||
| 59 : | my $prot = $cgi->param('prot'); | ||
| 60 : | if (! $prot) | ||
| 61 : | { | ||
| 62 : | push(@$html,"<h1>Sorry, you need to specify a protein</h1>\n"); | ||
| 63 : | &HTML::show_page($cgi,$html); | ||
| 64 : | exit; | ||
| 65 : | } | ||
| 66 : | |||
| 67 : | |||
| 68 : | if ($prot !~ /^fig\|/) | ||
| 69 : | { | ||
| 70 : | olson | 1.3.2.1 | my @poss = $fig_or_sprout->by_alias($prot); |
| 71 : | overbeek | 1.1 | if (@poss > 0) |
| 72 : | { | ||
| 73 : | $prot = $poss[0]; | ||
| 74 : | } | ||
| 75 : | else | ||
| 76 : | { | ||
| 77 : | push(@$html,"<h1>Sorry, $prot appears not to have a FIG id at this point</h1>\n"); | ||
| 78 : | &HTML::show_page($cgi,$html); | ||
| 79 : | exit; | ||
| 80 : | } | ||
| 81 : | } | ||
| 82 : | |||
| 83 : | olson | 1.3.2.1 | &compute_desired_homologs($fig_or_sprout,$cgi,$html,$prot); |
| 84 : | overbeek | 1.1 | &HTML::show_page($cgi,$html); |
| 85 : | exit; | ||
| 86 : | |||
| 87 : | sub compute_desired_homologs { | ||
| 88 : | olson | 1.3.2.1 | my($fig_or_sprout,$cgi,$html,$peg) = @_; |
| 89 : | overbeek | 1.1 | |
| 90 : | olson | 1.3.2.1 | my @pinned = &relevant_homologs($fig_or_sprout,$cgi,$peg); |
| 91 : | overbeek | 1.1 | # print STDERR &Dumper(\@pinned); |
| 92 : | |||
| 93 : | olson | 1.3.2.1 | # my @clusters = sort { (@$b <=> @$a) } &sets_of_homologs($fig_or_sprout,$cgi,$peg,\@pinned); |
| 94 : | overbeek | 1.1 | # print STDERR &Dumper(\@clusters); |
| 95 : | |||
| 96 : | overbeek | 1.3 | # my @homologs = &extract_homologs($peg,\@pinned,\@clusters); |
| 97 : | overbeek | 1.1 | # print STDERR &Dumper(\@homologs); |
| 98 : | |||
| 99 : | my $sc; | ||
| 100 : | my @tab = map { ($peg,$sc) = @$_; [$sc, | ||
| 101 : | &HTML::fid_link($cgi,$peg), | ||
| 102 : | olson | 1.3.2.1 | $fig_or_sprout->genus_species($fig_or_sprout->genome_of($peg)), |
| 103 : | scalar $fig_or_sprout->function_of($peg,$cgi->param('user')), | ||
| 104 : | &HTML::set_prot_links($cgi,join( ', ', $fig_or_sprout->feature_aliases($peg) )) | ||
| 105 : | overbeek | 1.3 | ] } @pinned; |
| 106 : | push(@$html,&HTML::make_table(["Score","PEG","Genome", "Function","Aliases"],\@tab,"PEGs that Might Be in Clusters")); | ||
| 107 : | overbeek | 1.1 | } |
| 108 : | |||
| 109 : | sub relevant_homologs { | ||
| 110 : | olson | 1.3.2.1 | my($fig_or_sprout,$cgi,$peg) = @_; |
| 111 : | overbeek | 1.1 | my($maxN,$maxP,$genome1,$sim,$id2,$genome2,%seen); |
| 112 : | |||
| 113 : | $maxN = $cgi->param('maxN'); | ||
| 114 : | $maxN = $maxN ? $maxN : 50; | ||
| 115 : | |||
| 116 : | $maxP = $cgi->param('maxP'); | ||
| 117 : | $maxP = $maxP ? $maxP : 1.0e-10; | ||
| 118 : | |||
| 119 : | olson | 1.3.2.1 | my @sims = $fig_or_sprout->sims( $peg, $maxN, $maxP, "fig"); |
| 120 : | overbeek | 1.1 | |
| 121 : | my @homologs = (); | ||
| 122 : | $seen{&FIG::genome_of($peg)} = 1; | ||
| 123 : | foreach $sim (@sims) | ||
| 124 : | { | ||
| 125 : | $id2 = $sim->id2; | ||
| 126 : | $genome2 = &FIG::genome_of($id2); | ||
| 127 : | overbeek | 1.3 | my @coup; |
| 128 : | olson | 1.3.2.1 | if ((! $seen{$genome2}) && (@coup = $fig_or_sprout->coupled_to($id2)) && (@coup > 0)) |
| 129 : | overbeek | 1.1 | { |
| 130 : | $seen{$genome2} = 1; | ||
| 131 : | overbeek | 1.3 | push(@homologs,[$id2,scalar @coup]); |
| 132 : | overbeek | 1.1 | } |
| 133 : | } | ||
| 134 : | overbeek | 1.3 | return sort { $b->[1] <=> $a->[1] } @homologs; |
| 135 : | overbeek | 1.1 | } |
| 136 : | |||
| 137 : | sub sets_of_homologs { | ||
| 138 : | olson | 1.3.2.1 | my($fig_or_sprout,$cgi,$given_peg,$pinned) = @_; |
| 139 : | overbeek | 1.1 | my($peg,$mid,$min,$max,$feat,$fid); |
| 140 : | |||
| 141 : | my $bound = $cgi->param('bound'); | ||
| 142 : | $bound = $bound ? $bound : 4000; | ||
| 143 : | |||
| 144 : | my @pegs = (); | ||
| 145 : | foreach $peg (($given_peg,@$pinned)) | ||
| 146 : | { | ||
| 147 : | olson | 1.3.2.1 | my $loc = $fig_or_sprout->feature_location($peg); |
| 148 : | overbeek | 1.1 | if ($loc) |
| 149 : | { | ||
| 150 : | my($contig,$beg,$end) = &FIG::boundaries_of($loc); | ||
| 151 : | if ($contig && $beg && $end) | ||
| 152 : | { | ||
| 153 : | $mid = int(($beg + $end) / 2); | ||
| 154 : | $min = $mid - $bound; | ||
| 155 : | $max = $mid + $bound; | ||
| 156 : | |||
| 157 : | olson | 1.3.2.1 | ($feat,undef,undef) = &genes_in_region($fig_or_sprout,$cgi,&FIG::genome_of($peg),$contig,$min,$max); |
| 158 : | overbeek | 1.1 | foreach $fid (@$feat) |
| 159 : | { | ||
| 160 : | if (&FIG::ftype($fid) eq "peg") | ||
| 161 : | { | ||
| 162 : | push(@pegs,$fid); | ||
| 163 : | } | ||
| 164 : | } | ||
| 165 : | } | ||
| 166 : | } | ||
| 167 : | } | ||
| 168 : | |||
| 169 : | my %represents; | ||
| 170 : | foreach $peg (@pegs) | ||
| 171 : | { | ||
| 172 : | olson | 1.3.2.1 | my $tmp = $fig_or_sprout->maps_to_id($peg); |
| 173 : | overbeek | 1.1 | push(@{$represents{$tmp}},$peg); |
| 174 : | olson | 1.3.2.1 | # if ($tmp ne $peg) { push(@{$represents{$peg}},$peg) } |
| 175 : | overbeek | 1.1 | } |
| 176 : | my($sim,%conn,$x,$y,$i,$j); | ||
| 177 : | foreach $y (keys(%represents)) | ||
| 178 : | { | ||
| 179 : | $x = $represents{$y}; | ||
| 180 : | for ($i=0; ($i < @$x); $i++) | ||
| 181 : | { | ||
| 182 : | for ($j=$i+1; ($j < @$x); $j++) | ||
| 183 : | { | ||
| 184 : | push(@{$conn{$x->[$i]}},$x->[$j]); | ||
| 185 : | push(@{$conn{$x->[$j]}},$x->[$i]); | ||
| 186 : | } | ||
| 187 : | } | ||
| 188 : | } | ||
| 189 : | |||
| 190 : | my $maxN = $cgi->param('maxN'); | ||
| 191 : | $maxN = $maxN ? $maxN : 50; | ||
| 192 : | |||
| 193 : | my $maxP = $cgi->param('maxP'); | ||
| 194 : | $maxP = $maxP ? $maxP : 1.0e-10; | ||
| 195 : | |||
| 196 : | foreach $peg (@pegs) | ||
| 197 : | { | ||
| 198 : | olson | 1.3.2.1 | foreach $sim ($fig_or_sprout->sims( $peg, $maxN, $maxP, "raw")) |
| 199 : | overbeek | 1.1 | { |
| 200 : | if (defined($x = $represents{$sim->id2})) | ||
| 201 : | { | ||
| 202 : | foreach $y (@$x) | ||
| 203 : | { | ||
| 204 : | push(@{$conn{$peg}},$y); | ||
| 205 : | } | ||
| 206 : | } | ||
| 207 : | } | ||
| 208 : | } | ||
| 209 : | |||
| 210 : | my(%seen,$k,$cluster); | ||
| 211 : | my @clusters = (); | ||
| 212 : | for ($i=0; ($i < @pegs); $i++) | ||
| 213 : | { | ||
| 214 : | $peg = $pegs[$i]; | ||
| 215 : | if (! $seen{$peg}) | ||
| 216 : | { | ||
| 217 : | $cluster = [$peg]; | ||
| 218 : | $seen{$peg} = 1; | ||
| 219 : | for ($j=0; ($j < @$cluster); $j++) | ||
| 220 : | { | ||
| 221 : | $x = $conn{$cluster->[$j]}; | ||
| 222 : | foreach $k (@$x) | ||
| 223 : | { | ||
| 224 : | if (! $seen{$k}) | ||
| 225 : | { | ||
| 226 : | push(@$cluster,$k); | ||
| 227 : | $seen{$k} = 1; | ||
| 228 : | } | ||
| 229 : | } | ||
| 230 : | } | ||
| 231 : | |||
| 232 : | if (@$cluster > 1) | ||
| 233 : | { | ||
| 234 : | push(@clusters,$cluster); | ||
| 235 : | } | ||
| 236 : | } | ||
| 237 : | } | ||
| 238 : | return @clusters; | ||
| 239 : | } | ||
| 240 : | |||
| 241 : | sub extract_homologs { | ||
| 242 : | my($given_peg,$pinned,$clusters) = @_; | ||
| 243 : | my(%main,$cluster,$peg,%counts,@with_counts); | ||
| 244 : | |||
| 245 : | %main = map { $_ => 1 } ($given_peg,@$pinned); | ||
| 246 : | foreach $cluster (@$clusters) | ||
| 247 : | { | ||
| 248 : | foreach $peg (@$cluster) | ||
| 249 : | { | ||
| 250 : | if (! $main{$peg}) | ||
| 251 : | { | ||
| 252 : | $counts{&FIG::genome_of($peg)} += @$cluster - 1; | ||
| 253 : | } | ||
| 254 : | } | ||
| 255 : | } | ||
| 256 : | |||
| 257 : | foreach $peg (($given_peg,@$pinned)) | ||
| 258 : | { | ||
| 259 : | push(@with_counts,[$peg,$counts{&FIG::genome_of($peg)}]); | ||
| 260 : | } | ||
| 261 : | |||
| 262 : | return grep { $_->[1] > 2} sort { $b->[1] <=> $a->[1] } @with_counts; | ||
| 263 : | } |
| MCS Webmaster | ViewVC Help |
| Powered by ViewVC 1.0.3 |