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1 #This is the TAp2.pl script
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2 #The goal of this is to count the number of CIS present in a NR set
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3 # one file is required nr.txt sorted in chromosome order!
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4 # Aaron Lyman Sarver Oct 21, 2010
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5 # This script takes over following the bowtie mapping and generates CIS.
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6 # Update NOV15,2010 to pass library information through
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7 #$Fully modified december 1 2010i
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8
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9 require 'config.pl';
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10 require 'lib/feature_finder_methods.pl';
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11 my $path = $0;
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12 $path =~ s/\/\w*\.pl$//g;
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13 require "$path/project_man.pl";
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14 unless (-d "CIS") {
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15 mkdir("CIS");
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16 }
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17 unless (-d "results") {
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18 mkdir("results");
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19 }
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20
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21 $proj_all = $proj."_all";
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22
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23 $sth = $dbh->prepare("drop table if exists lib_mappable_$proj_all");
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24 $sth->execute;
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25
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26 $sth = $dbh->prepare("drop table if exists lib_mappable_$proj");
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27 $sth->execute;
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28
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29 $sth = $dbh->prepare("drop table if exists illumina_hist_$proj_all");
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30 $sth->execute;
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31
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32 $sth = $dbh->prepare("drop table if exists illumina_hist_$proj");
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33 $sth->execute;
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34
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35 $sth = $dbh->prepare("drop table if exists bowtie_lib_$proj_all");
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36 $sth->execute;
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37
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38 $sth = $dbh->prepare("drop table if exists bowtie_lib_$proj");
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39 $sth->execute;
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40
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41 $sth = $dbh->prepare("drop table if exists metadata_$proj_all");
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42 $sth->execute;
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43
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44
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45 open DIN, "< data/meta.tab";
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46 @met;
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47 while (defined($line = <DIN>)) {
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48 chomp $line;
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49 @field= split(/\t/, $line);
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50 push (@met,$line);
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51 }
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52
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53 $proj_all = $proj."_all";
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54 $var=shift(@met);
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55
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56 $sth = $dbh->prepare("create table lib_mappable_$proj_all select * from lib_mappable_$var");
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57 $sth->execute;
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58 $sth = $dbh->prepare("create table illumina_hist_$proj_all select * from illumina_hist_$var");
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59 $sth->execute;
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60 $sth = $dbh->prepare("create table bowtie_lib_$proj_all select * from bowtie_lib_$var");
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61 $sth->execute;
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62 $sth = $dbh->prepare("create table metadata_$proj_all select * from metadata_$var");
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63 $sth->execute;
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64
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65 foreach $var(@met) {
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66 $sth = $dbh->prepare("insert into lib_mappable_$proj_all select * from lib_mappable_$var");
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67 $sth->execute;
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68 $sth = $dbh->prepare("insert into illumina_hist_$proj_all select * from illumina_hist_$var");
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69 $sth->execute;
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70 $sth = $dbh->prepare("insert into bowtie_lib_$proj_all select * from bowtie_lib_$var");
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71 $sth->execute;
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72 $sth = $dbh->prepare("insert into metadata_$proj_all select * from metadata_$var");
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73 $sth->execute;
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74 }
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75
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76 unless(-e "data/metadata.tab") {
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77 $sth = $dbh->prepare("select library, descriptor, type from metadata_$proj_all");
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78 $sth->execute;
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79 open(my $meta_out, ">", "data/metadata.tab") || die "Unable to open data/metadata.tab for output. $!\n";
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80 while ((@row) = $sth->fetchrow_array) {
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81 print $meta_out join("\t", @row) . "\n";
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82 }
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83 close($meta_out);
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84 }
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85
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86
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87 $sth = $dbh->prepare("create table lib_mappable_$proj select distinct library, sum(total) as total from lib_mappable_$proj_all group by library;");
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88 $sth->execute;
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89
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90 $sth = $dbh->prepare("create table illumina_hist_$proj select distinct library, chromo, start, sum(count) as count,orient from illumina_hist_$proj_all group by library,chromo,start,orient;");
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91 $sth->execute;
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92
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93 $sth = $dbh->prepare("create table bowtie_lib_$proj select distinct library,chromo, start,stop, pos, sum(count) as count,strand, orient from bowtie_lib_$proj_all group by library,chromo,start,stop,pos,strand order by chromo,start+0,orient ;");
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94 $sth->execute;
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95
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96 $sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj");
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97 $sth->execute;
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98 #7.2
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99 open OUT, "> results/raw_$proj.BED";
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100 print OUT "track type ='BED' name='raw$proj' description='all$proj' visibility=2 itemRgb='On'";
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101 while ((@row) = $sth->fetchrow_array) {
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102 print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]";}
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103 close OUT;
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104 #7.3
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105 $sth = $dbh->prepare("drop table if exists convert_2_hex_$proj");
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106 $sth->execute;
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107 $sth = $dbh->prepare("create table convert_2_hex_$proj (orient varchar(5), hex varchar(20))");
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108 $sth->execute;
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109 $sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"A\", \"255,0,0\")");
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110 $sth->execute;
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111 $sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"B\", \"0,0,255\")");
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112 $sth->execute;
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113 $sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"U\", \"0,0,0\")");
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114 $sth->execute;
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115
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116 $sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj where count > 9");
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117 ### JJE
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118 #$sth = $dbh->prepare("select chromo, start, start+1, concat(library,count),count,'+',start,start+1, hex from bowtie_lib_$proj A, convert_2_hex_$proj B where A.orient = B.orient and count > 9");
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119 ###
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120 $sth->execute;
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121 open OUT, "> results/raw10_$proj.BED";
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122 print OUT "track type ='BED' name='raw10$proj' description='10$proj' visibility=2 itemRgb='On'";
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123 while ((@row) = $sth->fetchrow_array) {
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124 print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]";}
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125 close OUT;
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126
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127 &set_project_status($proj, 1, 0);
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128
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