Metabolism Display

#!/usr/bin/perl -w use strict; use CGI qw(:standard); use CGI qw(param); # METABOLIC DISPLAY 2001 # ----------------------------- # Yale Gerstein Bioinformatics : Jimmy Lin # # A program to display metabolic information # and information associated with organisms # the code is very lazy and sloppy, please forgive (it works!) # USER SPECIFICATIONS #my $treename='ribosome'; # name of order #my @treeorder=qw(Mgen Hinf); # specification of order my $input= param("enzyme"); # my @treedata; my @treedata2; my $mi=0; if (!param("enzyme")){ $input="5.3.1.9"; } my $end; my $i; my $infoline; read_matrix("meta-table"); read_matrix2("meta-table2"); locate_enzyme("$input"); print_info("$infoline"); sub print_info { my ($i)=@_; print <Metabolism Display EndOfStart my $hvar = `perl /web/genecensus/header/header.cgi tree`; print "$hvar"; print ""; print "

"; #LEFT FRAME START print ""; #RIGHT FRAME START print ""; print "

"; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print "

"; for (my $m=2;$m<10;$m++){ print "$treedata[$m][1]
"; } print "

"; for (my $m=10;$m<15;$m++){ print "$treedata[$m][1]
"; } print "

"; for (my $m=15;$m<20;$m++){ print "$treedata[$m][1]
"; } print "

"; print "
"; print ""; print " Pathway View"; print ""; #LEFT FRAME END print "

"; print ""; print ""; print ""; print ""; print "

"; print ""; print "ENZYME: $treedata[$i][1] "; # print "(PATHWAY: $treedata[$i][0])"; print ""; print ""; print " $treedata[$i][1]"; print "
"; print "
"; print "FLUX VALUES
"; print "Flux variation (Standard deviation):$treedata2[$i][17]"; print ""; #"; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print "
Flux BSUB ECOL HPYL HINF SCER
BSUB ECOL HPYL HINF SCER
Normal $treedata[$i][2] $treedata[$i][3] $treedata[$i][4] $treedata[$i][5] $treedata[$i][6]
Absolute $treedata[$i][7] $treedata[$i][8] $treedata[$i][9] $treedata[$i][10] $treedata[$i][11]
Seq ID $treedata[$i][25] $treedata[$i][22] $treedata[$i][24] $treedata[$i][23] $treedata[$i][26]
"; #END TOP TABLE print "
"; print "PERCENTAGE IDENTITY
"; print "Average PID: $treedata2[$i][18]
"; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print "
% ID BSUB ECOL HPYL HINF SCER
BSUB 1.000 $treedata[$i][12] $treedata[$i][15] $treedata[$i][14] $treedata[$i][13]
ECOL $treedata[$i][12] 1.000 $treedata[$i][18] $treedata[$i][17] $treedata[$i][16]
HPYL $treedata[$i][15] $treedata[$i][14] 1.000 $treedata[$i][21] $treedata[$i][20]
HINF $treedata[$i][14] $treedata[$i][17] $treedata[$i][16] 1.000 $treedata[$i][19]
SCER $treedata[$i][13] $treedata[$i][16] $treedata[$i][20] $treedata[$i][19] 1.000
"; print "
"; print "EXPRESSION DATA
"; print "Multi-scale Reference: $treedata[$i][27] copies per cell

"; print "Standard Deviation of Expression Change"; print ""; for ($mi=2;$mi<9;$mi++){ print ""; } print ""; for ($mi=2;$mi<9;$mi++){ print ""; } print "
Experiment $treedata2[1][$mi]
STDEV $treedata2[$i][$mi]
"; print "Average of Expression Change"; print ""; for ($mi=9;$mi<17;$mi++){ print ""; } print ""; for ($mi=9;$mi<17;$mi++){ print ""; } print "
Experiment $treedata2[1][$mi]
STDEV $treedata2[$i][$mi]
"; print "
"; print "EXPRESSION TIMEPOINTS
"; print "Mitotic Cell Cycle [normalized transcript level divided by mean value] "; print "link"; print ""; print ""; print ""; print ""; print ""; print ""; print "
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
$treedata[$i][28] $treedata[$i][29] $treedata[$i][30] $treedata[$i][31] $treedata[$i][32] $treedata[$i][33] $treedata[$i][34] $treedata[$i][35] $treedata[$i][36] $treedata[$i][37] $treedata[$i][38] $treedata[$i][39] $treedata[$i][40] $treedata[$i][41] $treedata[$i][42] $treedata[$i][43] $treedata[$i][44]
"; print "Alpha Factor Arrest Synchronization [log2(ratio of mRNA levels)] "; print "link"; print ""; print ""; print ""; print ""; print ""; print ""; print "
0 7 14 21 28 35 42 49 56 63 70 77 84 91 98 105 112 119
$treedata[$i][49] $treedata[$i][50] $treedata[$i][51] $treedata[$i][52] $treedata[$i][53] $treedata[$i][54] $treedata[$i][55] $treedata[$i][56] $treedata[$i][57] $treedata[$i][58] $treedata[$i][59] $treedata[$i][60] $treedata[$i][61] $treedata[$i][62] $treedata[$i][63] $treedata[$i][64] $treedata[$i][65] $treedata[$i][66]
"; print "CDC15 Synchronization [log2(ratio of mRNA levels)] "; print "link"; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print ""; print "
10 30 50 70 80 90 100 110 120 130 140 150 160
$treedata[$i][67] $treedata[$i][68] $treedata[$i][69] $treedata[$i][70] $treedata[$i][71] $treedata[$i][72] $treedata[$i][73] $treedata[$i][74] $treedata[$i][75] $treedata[$i][76] $treedata[$i][77] $treedata[$i][78] $treedata[$i][79]
170 180 190 200 210 220 230 240 250 270 290
$treedata[$i][80] $treedata[$i][81] $treedata[$i][82] $treedata[$i][83] $treedata[$i][84] $treedata[$i][85] $treedata[$i][86] $treedata[$i][87] $treedata[$i][88] $treedata[$i][89] $treedata[$i][90]
"; print "CDC28 (Stanford) [log2(ratio of mRNA levels)] "; print ""; print ""; print ""; print ""; print ""; print ""; print "
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
$treedata[$i][91] $treedata[$i][92] $treedata[$i][93] $treedata[$i][94] $treedata[$i][95] $treedata[$i][96] $treedata[$i][97] $treedata[$i][98] $treedata[$i][99] $treedata[$i][100] $treedata[$i][101] $treedata[$i][102] $treedata[$i][103] $treedata[$i][104] $treedata[$i][105] $treedata[$i][106] $treedata[$i][107]
"; print "Elutration Synchronization [log2(ratio of mRNA levels)] "; print "link"; print ""; print ""; print ""; print ""; print ""; print "
0 30 60 90 120 150 180 210 240 270 300 330 360 390
$treedata[$i][108] $treedata[$i][109] $treedata[$i][110] $treedata[$i][111] $treedata[$i][112] $treedata[$i][113] $treedata[$i][114] $treedata[$i][115] $treedata[$i][116] $treedata[$i][17] $treedata[$i][101] $treedata[$i][102] $treedata[$i][103] $treedata[$i][104]
"; print "

"; print "
"; print "

"; print ""; #RIGHT FRAME END print ""; #TABLE END print ""; } sub locate_enzyme { my ($name)=@_; $end-=2; for ($i=2; $i<$end; $i++) { # print "$treedata[$i][1]"; if ($input eq $treedata[$i][1]){ # print " BANG!"; $infoline=$i; } # print "\n"; } } sub read_matrix { my ($filename)=@_; open (DATA, "./$filename.txt") or die "cannot open $filename.txt"; my $tree_chunk; my @store_array; my $x=0; my $y=0; while () { $y=0; for $tree_chunk (split()){ # print "$tree_chunk "; $treedata[$x][$y]=$tree_chunk; $y++; } $end=$y; # print "\n"; $x++; } close DATA; } sub read_matrix2 { my ($filename)=@_; open (DATA, "./$filename.txt") or die "cannot open $filename.txt"; my $tree_chunk; my @store_array; my $x=0; my $y=0; while () { $y=0; for $tree_chunk (split()){ # print "$tree_chunk "; $treedata2[$x][$y]=$tree_chunk; $y++; } $end=$y; # print "\n"; $x++; } close DATA; }