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comparison tools/rdock/bin/ht_protocol_finder.pl @ 3:b02d74d22d05 draft default tip

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planemo upload
author marpiech
date Mon, 29 Aug 2016 08:23:52 -0400
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2:bd50f811878f 3:b02d74d22d05
1 #!/usr/bin/perl -w
2
3 # Script that simulates the result of a high throughput protocol.
4
5 if (@ARGV < 4)
6 {
7 print "Script that simulates the result of a high throughput protocol.\n";
8 print "1st) exhaustive docking of a small representative part of the\n";
9 print " whole library.\n";
10 print "2nd) Store the result of sdreport -t over that exhaustive dock.\n";
11 print " in file <sdreport_file> that will be the input of this\n";
12 print " script.\n";
13 print "3rd) ht_protocol_finder.pl <sdreport_file> <output_file> <thr1max>";
14 print " <thr1min> <ns1> <ns2>\n";
15 print " <ns1> and <ns2> are the number of steps in stage 1 and in\n";
16 print " stage 2. If not present, the default values are 5 and 15\n";
17 print " <thrmax> and <thrmin> setup the range of thresholds that will\n";
18 print " be simulated in stage 1. The threshold of stage 2 depends\n";
19 print " on the value of the threshold of stage 1.\n";
20 print " An input of -22 -24 will try protocols:\n";
21 print " 5 -22 15 -27\n";
22 print " 5 -22 15 -28\n";
23 print " 5 -22 15 -29\n";
24 print " 5 -23 15 -28\n";
25 print " 5 -23 15 -29\n";
26 print " 5 -23 15 -30\n";
27 print " 5 -24 15 -29\n";
28 print " 5 -24 15 -30\n";
29 print " 5 -24 15 -31\n";
30 print " Output of the program is a 7 column values. First column\n";
31 print " represents the time. This is a percentage of the time it\n";
32 print " would take to do the docking in exhaustive mode, i.e. \n";
33 print " docking each ligand 100 times. Anything\n";
34 print " above 12 is too long.\n";
35 print " Second column is the first percentage. Percentage of\n";
36 print " ligands that pass the first stage.\n";
37 print " Third column is the second percentage. Percentage of\n";
38 print " ligands that pass the second stage.\n";
39 print " The four last columns represent the protocol.\n";
40 print " All the protocols tried are written at the end.\n";
41 print " The ones for which time is less than 12%, perc1 is\n";
42 print " less than 30% and perc2 is less than 5% but bigger than 1%\n";
43 print " will have a series of *** after, to indicate they are good choices\n";
44 print " WARNING! This is a simulation based in a small set.\n";
45 print " The numbers are an indication, not factual values.\n";
46 exit (0);
47 }
48 open (IFILE, $ARGV[0]) || die "cannot open $ARGV[0] for reading: $!";
49 open (OFILE, ">$ARGV[1]") || die "cannot open $ARGV[1] for writing: $!";
50 <IFILE>; # read first line
51 $line = <IFILE>;
52 $line =~ /\S+\s+(\S+)\s+\S+\s+(\S+)/;
53 $prevname = $1;
54 $inter = $2;
55 push @tmp, $inter;
56 $i = 0;
57 while ($line = <IFILE>)
58 {
59 $line =~ /\S+\s+(\S+)\s+\S+\s+(\S+)/;
60 $name = $1;
61 $inter = $2;
62 if ($name ne $prevname)
63 {
64 $prevname = $name;
65 push @inters, [ @tmp ];
66 $runsperligand[$i++] = @tmp;
67 $#tmp = -1;
68 }
69 push @tmp, $inter;
70 }
71 push @inters, [ @tmp ];
72 $runsperligand[$i++] = @tmp;
73 $totLigands = @inters;
74 $ta = $ARGV[2];
75 $tb = $ARGV[3];
76 if (@ARGV > 4)
77 {
78 $n1 = $ARGV[4];
79 }
80 else
81 {
82 $n1 = 5;
83 }
84 if (@ARGV > 5)
85 {
86 $n2 = $ARGV[5];
87 }
88 else
89 {
90 $n2 = 15;
91 }
92 printf OFILE "Command line args:\n\t";
93 foreach $arg (@ARGV)
94 {
95 printf OFILE "%s\t", $arg;
96 }
97 printf OFILE "\n\n TIME PERC1 PERC2 N1 THR1 N2 THR2\n";
98 for ($t1 = $ta ; $t1 >= $tb ; $t1--)
99 {
100 $tc = $t1 - 5;
101 for ($t2 = $tc ; $t2 >= ($tc - 2) ; $t2--)
102 {
103 ($cref, $dref) =
104 getTables($t1, $t2);
105 @ligBelowThr1 = @$cref;
106 @ligBelowThr2 = @$dref;
107 ($time,$p1,$p2) = simulation($n1,$t1,$n2,$t2);
108 if (($time < 12.0) && ($p1 < 30.0) && ($p2 < 5.0) && ($p2 > 1.0))
109 {
110 printf OFILE "%6.3f, %6.3f, %6.3f, %4i, %4i, %4i, %4i ***\n",
111 $time, $p1, $p2, $n1,$t1,$n2,$t2;
112 }
113 else
114 {
115 printf OFILE "%6.3f, %6.3f, %6.3f, %4i, %4i, %4i, %4i\n",
116 $time, $p1, $p2, $n1,$t1,$n2,$t2;
117 }
118 }
119 }
120
121
122 sub simulation
123 {
124 my(@params);
125 my(@lt0, @lt1);
126 my($thr1, $thr2,$ns1,$ns2,$tottime,$totnumHits,$total,$totnruns);
127 @params = @_;
128 $ns1 = $params[0];
129 $thr1 = $params[1];
130 $ns2 = $params[2];
131 $thr2 = $params[3];
132 $ntrials = 100;
133 $tottime = 0;
134 $totnumHitss1 = 0;
135 $totnumHitss2 = 0;
136 $total = $totLigands;
137 $totnruns = 0;
138 for ($i = 0 ; $i < $ntrials ; $i++)
139 {
140 $numHitss1 = 0;
141 $numHitss2 = 0;
142 $totnruns = 0;
143 for ($j = 0 ; $j < $totLigands ; $j++)
144 {
145 ($passStage1, $nruns1) = stage($ns1, $ligBelowThr1[$j]);
146 if ($passStage1)
147 {
148 $numHitss1++;
149 ($passStage2, $nruns2) = stage($ns2, $ligBelowThr2[$j]);
150 if ($passStage2)
151 {
152 $numHitss2++;
153 }
154 $totnruns += $nruns2;
155 }
156 $totnruns += $nruns1;
157 }
158 $time = $totnruns / $total;
159 $tottime += $time;
160 $totnumHitss1 += $numHitss1;
161 $totnumHitss2 += $numHitss2;
162 }
163 $tottime /= $ntrials;
164 $totnumHitss1 /= $ntrials;
165 $totnumHitss2 /= $ntrials;
166 $p1 = $totnumHitss1 * 100.0 / $totLigands;
167 $p2 = $totnumHitss2 * 100.0 / $totLigands;
168 return ($tottime, $p1, $p2);
169 }
170
171 sub getTables
172 {
173 my(@params);
174 my($totLigands, @lt1, @lt2);
175 my($row,$inter, $belowThr1, $belowThr2);
176 my($thr0, $thr1);
177 @params = @_;
178 $thr1 = $params[0];
179 $thr2 = $params[1];
180 $totLigands = 0;
181 $belowThr1 = 0;
182 $belowThr2 = 0;
183 $totLigands = 0;
184 for $i (0 .. $#inters)
185 {
186 $row = $inters[$i];
187 for $j (0 .. $#{$row})
188 {
189 $inter = $row->[$j];
190 if ($inter <= $thr1)
191 {
192 $belowThr1++;
193 }
194 if ($inter <= $thr2)
195 {
196 $belowThr2++;
197 }
198 }
199 $lt1[$totLigands] =
200 $belowThr1 / $runsperligand[$i];
201 $lt2[$totLigands] =
202 $belowThr2 / $runsperligand[$i];
203 $totLigands++;
204 $belowThr1 = 0;
205 $belowThr2 = 0;
206 }
207 return (\@lt1, \@lt2);
208 }
209
210
211
212 sub stage
213 {
214 my($nruns, $p, $i, $r);
215 $nruns = $_[0];
216 $p = $_[1];
217 if ($nruns == 0)
218 {
219 return (1, 0);
220 }
221 for ($i = 0 ; $i < $nruns ; $i++)
222 {
223 $r = rand;
224 if ($r < $p)
225 {
226 return (1, $i);
227 }
228 }
229 return (0, $nruns);
230 }
231
232