Mercurial > repos > jesse-erdmann > tapdance

comparison lib/visualize.pl @ 0:1437a2df99c0

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jesse-erdmann
date Fri, 09 Dec 2011 11:56:56 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1437a2df99c0
1 require 'config.pl';
2 open OUT, "> FISH/library_cis_list.txt";
3 open OUT2, ">FISH/multi_test.txt";
4
5 $query1 = "select count(name) from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100";
6 $sth = $dbh->prepare("$query1");
7
8 $sth->execute;
9
10 while ((@row) = $sth->fetchrow_array) {
11 $cis_number = $row[0];
12 }
13
14 $query2="select name,gene_name, library_name from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100";
15
16 $sth = $dbh->prepare("$query2");
17 $sth->execute;
18
19 while ((@row) = $sth->fetchrow_array) {
20 #print $row[2];
21 @chunks = split(/::/m, $row[2]);
22 foreach $lib(@chunks) {
23 if ($lib ne '') {
24 print OUT "$row[0]::$row[1]\t$lib\t1\n";
25 }
26 }
27 }
28 close OUT;
29
30 $sth = $dbh->prepare("select count(distinct descriptor) from metadata_$proj where descriptor != 'all';");
31
32 $sth->execute;
33
34 while ((@row) = $sth->fetchrow_array) {
35 $desc_number = $row[0];
36 }
37 $ann_cis_testing = $desc_number*$cis_number;
38 $cis_cis_testing = $cis_number*($cis_number-3)/2;
39 $ann_ann_testing = $desc_number*($desc_number-3)/2;
40 print OUT2 "$cis_number\t$desc_number\t$ann_cis_testing\t$cis_cis_testing\t$ann_ann_testing\n";
41 close OUT2;
42 $sth = $dbh->prepare("select 'descriptor', descriptor, library from metadata_$proj;");
43 $sth->execute;
44
45 open OUT, "> FISH/library_descriptor_list.txt";
46
47 while ((@row) = $sth->fetchrow_array) {
48 print OUT "$row[0]::$row[1]\t$row[2]\t1\n";
49 }
50
51 close OUT;
52
53 open (my $list, ">", "FISH/list.txt");
54 open (my $cis_list, "<", "FISH/library_cis_list.txt");
55 while(<$cis_list>) {
56 print $list $_;
57 }
58 close($cis_list);
59 open (my $desc_list, "<", "FISH/library_descriptor_list.txt");
60 while (<$desc_list>) {
61 print $list $_;
62 }
63 close($desc_list);
64 close($list);
65 #system ("cat FISH/library_cis_list.txt FISH/library_descriptor_list.txt > FISH/list.txt");
66 system ("perl lib/list2tab.pl 1 2 3 0 FISH/list.txt > FISH/cis4cluster.txt");
67 system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_cis_list.txt > results/Assoc/Cis.txt");
68 system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_descriptor_list.txt > results/Assoc/Ann.txt");
69
70 print "generated the matrix file cis4cluster.txt";
71
72