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1 use strict;
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2 use List::Util qw[min max];
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3
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4 my $all = "ALL";
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5 my $close = "CLOSEST";
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6 my $first_idx = 0;
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7 my $left = -1;
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8 my $right = 1;
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9 my $both = 0;
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10 my $keys = "KEYS";
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11 my $NOT_FOUND = -3;
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12 my $NOT_FOUND_STR = "NOT FOUND";
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13 my $ENCOMPASSING = -2;
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14 #my $ENCOMPASSING_STR = "";
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15 my $ENCOMPASSING_STR = "ENCOMPASSING FEATURE";
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16 my $INTERNAL = -1;
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17 #my $INTERNAL_STR = "";
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18 my $INTERNAL_STR = "INTERNAL FEATURE";
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19
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20 return 1;
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21
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22 sub feature_index {
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23 my ($feature_file, $window, $fchrom_col, $fstart_col, $fend_col, $debug) = @_;
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24 open(FEATURES, "<${$feature_file}") || die "Unable to open features file, ${$feature_file}: $!\n";
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25 my %feature_hash = ();
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26 my $num_indexed = 0;
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27 while (<FEATURES>) {
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28 if (${$debug}) {
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29 if (($num_indexed % 1000) == 0) {
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30 my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time);
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31 print sprintf("%02d-%02d %02d:%02d:%02d Features Indexed: %9s\n", ($mon+1), $day, $hour, $min, $sec, $num_indexed);
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32 }
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33 }
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34 chomp;
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35 $num_indexed++;
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36 my @split_line = split("\t");
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37 if (!@split_line) { next; }
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38 my $interim_hash1 = int($split_line[${$fstart_col}]/${$window});
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39 my $interim_hash2 = int($split_line[${$fend_col}]/${$window});
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40 for (my $interim_hash = min($interim_hash1, $interim_hash2); $interim_hash <= max($interim_hash1, $interim_hash2); $interim_hash++) {
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41 push @{$feature_hash{$split_line[${$fchrom_col}]}->{$interim_hash}->{$split_line[${$fstart_col}]}}, \@split_line;
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42 }
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43 }
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44 close(FEATURES);
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45 if (${$debug}) { print "$num_indexed indexed\n"; }
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46
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47 my $min_keys_in_window;
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48 my $max_keys_in_window;
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49 my $num_idxs = 0;
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50 my $total_keys = 0;
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51 foreach my $chrom (keys %feature_hash) {
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52 foreach my $interim_hash (keys %{$feature_hash{$chrom}}) {
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53 $num_idxs++;
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54 my @sorted_keys = sort {$a <=> $b} keys %{$feature_hash{$chrom}->{$interim_hash}};
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55 my $interim_key = join("_", ($interim_hash, $keys));
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56 my $num_keys = $#sorted_keys+1;
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57 #print OUT "interim_hash:$interim_hash interim_key:$interim_key num_keys:$num_keys @sorted_keys\n";
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58 $feature_hash{$chrom}->{$interim_key} = \@sorted_keys;
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59 $total_keys += $#sorted_keys + 1;
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60 if (!defined($min_keys_in_window) || ($#sorted_keys+1) < $min_keys_in_window) { $min_keys_in_window = ($#sorted_keys+1); }
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61 if (!defined($max_keys_in_window) || ($#sorted_keys+1) > $max_keys_in_window) { $max_keys_in_window = ($#sorted_keys+1); }
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62 }
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63 }
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64 if (${$debug}) {
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65 my $avg_keys = $total_keys/$num_idxs;
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66 print "Smallest # of keys in window: $min_keys_in_window, Largest: $max_keys_in_window $total_keys in $num_idxs windows for an average of $avg_keys\n";
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67 }
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68
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69 return \%feature_hash;
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70 }
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71
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72 sub process_intervals {
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73 my ($intervals_file, $out_file, $feature_hash_ref, $req_res_type_ref, $direction_ref, $window_ref, $html_ref, $cturl_ref, $db_ref, $icols_ref, $fcols_ref, $debug_ref, $dd_ref, $capture, $promoter) = @_;
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74 if (${$debug_ref}) { print sprintf("process_intervals(intervals:%s, out:%s, direction:%s, window:%s, icols_ref:%s)\n", ${$intervals_file}, ${$out_file}, ${$direction_ref}, ${$window_ref}, ${$icols_ref}); }
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75 open(INTERVALS, "<${$intervals_file}") || die "Unable to open intervals file, ${$intervals_file}: $!\n";
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76 open(my $out_h, ">${$out_file}") || die "Unable to open output file, ${$out_file}: $!\n";
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77
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78 #if (${$debug_ref}) { print sprintf("%s features in index.\n", keys %{$feature_hash_ref}); }
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79
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80 my @icols = split(":", ${$icols_ref});
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81 #pod2usage({ message => "Must specify 5 columns with -icol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#icols != 4);
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82 my $ichrom = $icols[0]-1;
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83 my $istart = $icols[1]-1;
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84 my $iend = $icols[2]-1;
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85 my $ilabel = $icols[3]-1;
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86 my $istrand = $icols[4]-1;
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87
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88 my @fcols = split(":", ${$fcols_ref});
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89 #pod2usage({ message => "Must specify 5 columns with -fcol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#fcols != 4);
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90 my $fchrom = $fcols[0]-1;
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91 my $fstart = $fcols[1]-1;
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92 my $fend = $fcols[2]-1;
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93 my $flabel = $fcols[3]-1;
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94 my $fstrand = $fcols[4]-1;
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95
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96 my $cturl;
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97 my $print = \&print_res;
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98 if (${$html_ref}) {
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99 $print = \&print_res_html;
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100 print $out_h "<HTML>\n<HEAD>\n\t<TITLE>Feature Finder Annotation</TITLE>\n</HEAD>\n<BODY>\n<TABLE>\n";
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101 if (defined(${$cturl_ref})) {
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102 ${$cturl} =~ s/X26/\%26/g;
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103 }
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104 }
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105
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106 my $count = 0;
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107 foreach (<INTERVALS>) {
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108 if (${$debug_ref}) {
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109 if (($count % 1000) == 0) {
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110 my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time);
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111 print sprintf("%02d-%02d %02d:%02d:%02d Intervals Processed: %9s\n", ($mon+1), $day, $hour, $min, $sec, $count);
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112 }
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113 $count++;
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114 }
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115 chomp;
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116 my @split_line = split("\t");
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117 if (!@split_line) { next; }
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118 if (!defined(${$feature_hash_ref}{$split_line[$ichrom]})) {
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119 #if (${$debug_ref}) { print "."; }
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120 next;
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121 }
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122 my $win_start = min($split_line[$istart], $split_line[$iend]) - ${$window_ref};
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123 if ($win_start < 0) { $win_start = 0; }
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124 my $start_idx = int($win_start/${$window_ref}) -1;
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125 if ($start_idx < 0) { $start_idx = 0; }
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126 my $win_end = max($split_line[$istart], $split_line[$iend]) + ${$window_ref};
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127 my $end_idx = int($win_end/${$window_ref}) +1;
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128
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129 if (uc ${$req_res_type_ref} eq $all) {
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130 &$print(\$out_h, \@split_line, \$istart, \$iend, &compare(\$out_h, $feature_hash_ref, \$all, \@split_line, \$split_line[$ichrom], \$win_start, \$win_end, \$start_idx, \$end_idx, \$both, \$ichrom, \$istart, \$iend, \$ilabel, \$istrand, \$fchrom, \$fstart, \$fend, \$flabel, $debug_ref), \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom, \$istart, \$iend);
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131 }
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132 else {
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133 my %left_res = ();
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134 my %right_res = ();
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135 #if (${$debug_ref}) { print sprintf("STRAND:%s\tDIRECTION:%s\n", $split_line[$istrand], ${$direction_ref}); }
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136 if ($split_line[$istrand] ne "+" && $split_line[$istrand] ne "-") { warn sprintf("Found \"%s\" as the strand of %s:%s-%s %s, please verify icols match your input data\n", $split_line[$istrand], $split_line[$ichrom], $split_line[$istart], $split_line[$iend], $split_line[$ilabel]); }
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137 if (($split_line[$istrand] eq "+" && uc ${$direction_ref} ne "DOWNSTREAM") || ($split_line[$istrand] eq "-" && uc ${$direction_ref} ne "UPSTREAM")) {
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138 %left_res = %{&compare(\$out_h, $feature_hash_ref, \$close, \@split_line, \$split_line[$ichrom], \$win_start, \$win_end, \$start_idx, \$end_idx, \$left, \$ichrom, \$istart, \$iend, \$ilabel, \$istrand, \$fchrom, \$fstart, \$fend, \$flabel, $debug_ref)};
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139 }
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140 if (($split_line[$istrand] eq "-" && uc ${$direction_ref} ne "DOWNSTREAM") || ($split_line[$istrand] eq "+" && uc ${$direction_ref} ne "UPSTREAM")) {
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141 %right_res = %{&compare(\$out_h, $feature_hash_ref, \$close, \@split_line, \$split_line[$ichrom], \$win_start, \$win_end, \$start_idx, \$end_idx, \$right, \$ichrom, \$istart, \$iend, \$ilabel, \$istrand, \$fchrom, \$fstart, \$fend, \$flabel, $debug_ref)};
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142 }
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143 if (keys %left_res == 0) {
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144 &$print(\$out_h, \@split_line, \$istart, \$iend, \%right_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom);
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145 }
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146 elsif (keys %right_res == 0) {
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147 &$print(\$out_h, \@split_line, \$istart, \$iend, \%left_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom);
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148 }
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149 else {
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150 my @left_keys = keys %left_res;
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151 my @right_keys = keys %right_res;
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152 if (uc ${$direction_ref} eq "BOTH") {
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153 @left_res{keys %right_res} = values %right_res;
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154 &$print(\$out_h, \@split_line, \$istart, \$iend, \%left_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom);
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155 }
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156 else {
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157 if ($left_keys[0] <= $right_keys[0]) {
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158 &$print(\$out_h, \@split_line, \$istart, \$iend, \%left_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom);
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159 }
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160 elsif ($right_keys[0] < $left_keys[0]) {
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161 &$print(\$out_h, \@split_line, \$istart, \$iend, \%right_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom);
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162 }
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163 }
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164 }
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165 }
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166 }
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167 close(INTERVALS);
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168 if (${$html_ref}) {
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169 print $out_h "</TABLE>\n</BODY>\n</HTML>\n";
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170 }
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171 close($out_h);
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172
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173 }
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174
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175 sub compare {
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176 my ($out_h_ref, $feature_hash_ref, $res_type, $interval_array_ref, $chrom, $window_start, $window_end, $start_idx, $end_idx, $direction, $ichrom, $istart, $iend, $ilabel, $istrand, $fchrom, $fstart, $fend, $flabel, $debug) = @_;
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177 #if (${$debug}) { print sprintf("compare(result type:%s, chrom:%s, win start:%s, win end:%s, direction:%s, ichrom_col:%s, fchrom_col:%s, ilabel_col:%s, flabel_col:%s, debug:%s)\n", ${$res_type}, ${$chrom}, ${$window_start}, ${$window_end}, ${$direction}, ${$ichrom}, ${$fchrom}, ${$ilabel}, ${$flabel}, ${$debug}); }
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178 my %result = ();
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179 my %reshash = ();
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180 my $feature_start;
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181 my $feature_end;
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182 my $interval_start;
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183 my $interval_end;
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184 my $interval_idx;
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185 my $best_distance = $NOT_FOUND;
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186 for ($interval_idx = ${$start_idx}; $interval_idx <= ${$end_idx}; $interval_idx++) {
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187 my $interval_key = join("_", ($interval_idx, $keys));
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188 if (!defined(${$feature_hash_ref}{${$chrom}}->{$interval_key})) {
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189 next;
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190 }
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191
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192 my @feature_keys = @{${$feature_hash_ref}{${$chrom}}->{$interval_key}};
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193 my $interval_midp = (($interval_array_ref->[${$istart}] + $interval_array_ref->[${$iend}])/2);
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194 foreach my $feature_idx (@feature_keys) {
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195 foreach my $feature (@{${$feature_hash_ref}{${$chrom}}->{$interval_idx}->{$feature_idx}}) {
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196 $feature_start = min($feature->[${$fstart}], $feature->[${$fend}]);
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197 $feature_end = max($feature->[${$fstart}], $feature->[${$fend}]);
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198 $interval_start = min($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]);
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199 $interval_end = max($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]);
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200 my $reskey = join(":", ($interval_array_ref->[${$ichrom}], ${$window_start}, ${$window_end}, $interval_array_ref->[${$ilabel}], $feature->[${$fchrom}], $feature_start, $feature_end, $feature->[${$flabel}]));
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201 my $distance;
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202 if ($feature_start <= $interval_start && $feature_end >= $interval_end) { $distance = $ENCOMPASSING; }
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203 elsif ($interval_start < $feature_start && $interval_end > $feature_end) { $distance = $INTERNAL; }
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204 else {
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205 $distance = min(abs($interval_array_ref->[${$istart}] - $feature_start), abs($interval_array_ref->[${$istart}] - $feature_end), abs($interval_array_ref->[${$iend}] - $feature_start), abs($interval_array_ref->[${$iend}] - $feature_end));
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206 #if (${$debug}) { print "FEATURE:$feature->[${$flabel}]\tDISTANCE:$distance\n"; }
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207 }
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208 my $dir_str = "";
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209 my $feature_midp = ($feature_start + $feature_end)/2;
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210 if ($interval_midp >= $feature_midp) {
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211 if ($interval_array_ref->[${$istrand}] eq "+") { $dir_str = "UPSTREAM"; }
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212 else { $dir_str = "DOWNSTREAM" }
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213 }
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214 else {
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215 if ($interval_array_ref->[${$istrand}] eq "-") { $dir_str = "UPSTREAM"; }
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216 else { $dir_str = "DOWNSTREAM" }
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217 }
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218
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219 if (${$res_type} eq $close) {
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220 if (${$direction} == $left) {
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221 if ($interval_midp < $feature_midp) { next; }
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222 }
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223 elsif (${$direction} == $right) {
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224 if ($interval_midp >= $feature_midp) { next; }
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225 }
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226
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227 #print ${$out_h_ref} "distance:$distance best_distance:$best_distance\n";
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228 if ($best_distance > $NOT_FOUND) {
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229 if ($distance < $best_distance) {
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230 delete $result{$best_distance};
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231 if (!defined($reshash{$reskey})) {
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232 $reshash{$reskey} = $feature;
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233 push @{$result{$distance}{$feature->[${$flabel}]}}, $feature, $dir_str;
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234 #$result{$distance}{$feature->[${$flabel}]} = $dir_str;
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235 $best_distance = $distance;
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236 }
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237 }
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238 }
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239 else {
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240 if (!defined($reshash{$reskey})) {
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241 $reshash{$reskey} = $feature;
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242 push @{$result{$distance}{$feature->[${$flabel}]}}, $feature, $dir_str;
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243 #$result{$distance}{$feature->[${$flabel}]} = $dir_str;
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244 $best_distance= $distance;
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245 }
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246 }
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247 }
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248 else {
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249 # if the interval start - the window is less than the end of the feature and the interval end + the window is greater than the start of the feature it's included
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250 if (${$window_start} <= $feature_end && ${$window_end} >= $feature_start) {
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251 if (!defined($reshash{$reskey})) {
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252 $reshash{$reskey} = $feature;
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253 push @{$result{$distance}{$feature->[${$flabel}]}}, $feature, $dir_str;
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254 #$result{$distance}{$feature->[${$flabel}]} = $dir_str;
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255 }
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256 }
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257 }
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258 }
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259 }
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260 }
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261 return \%result;
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262 }
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263
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264 sub print_res {
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265 my ($out_h_ref, $interval_array_ref, $istart, $iend, $result_hash_ref, $flabel, $fstart, $fend, $fstrand, $window, $promoter_len, $capture, $dd_ref) = @_;
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266 print ${$out_h_ref} join("\t", @{$interval_array_ref});
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267 my @sorted_keys = sort {$a <=> $b} keys %{$result_hash_ref};
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268 if (defined($sorted_keys[0])) {
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269 print ${$out_h_ref} sprintf("\t");
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270 my $left_end = $interval_array_ref->[${$istart}];
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271 my $right_end = $interval_array_ref->[${$iend}];
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272 my $fstart_pos;
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273 my $fend_pos;
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274 foreach my $next_key (@sorted_keys) {
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275 foreach my $res (keys %{$result_hash_ref->{$next_key}}) {
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276 #my @feature_keys = keys %{$res};
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277 if (defined($capture) && ${$capture}) {
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278 if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '+') {
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279 $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}] - ${$promoter_len};
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280 } else {
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281 $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}];
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282 }
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283 if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '-') {
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284 $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}] + ${$promoter_len};
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285 } else {
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286 $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}];
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287 }
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288 if ($fstart_pos < $left_end) { $left_end = $fstart_pos; }
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289 if ($fend_pos > $right_end) { $right_end = $fend_pos; }
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290 }
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291 if (!${$dd_ref}) {
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292 print ${$out_h_ref} sprintf("%s, ", $res);
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293 } else {
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294 if ($next_key == $ENCOMPASSING) {
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295 print ${$out_h_ref} sprintf("%s (%s), ", $res, $ENCOMPASSING_STR);
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296 }
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297 elsif ($next_key == $INTERNAL) {
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298 print ${$out_h_ref} sprintf("%s (%s), ", $res, $INTERNAL_STR);
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299 }
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300 else {
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301 print ${$out_h_ref} sprintf("%s (%s bp %s), ", $res, $next_key, @{$result_hash_ref->{$next_key}->{$res}}[1]);
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302 }
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303 }
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304 }
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305 }
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306 if (defined($capture) && ${$capture}) {
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307 print ${$out_h_ref} sprintf("\t%s\t%s\t%s", $left_end, $right_end, $right_end - $left_end);
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308 }
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309 }
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310 else {
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311 print ${$out_h_ref} sprintf("\tNo results within ${$window} bp window");
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312 }
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313 print ${$out_h_ref} sprintf("\n");
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314 }
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315
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316 sub print_res_html {
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317 my ($out_h_ref, $interval_array_ref, $istart, $iend, $result_hash_ref, $flabel, $fstart, $fend, $fstrand, $window, $promoter_len, $capture, $dd_ref, $db, $cturl, $ichrom) = @_;
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318 print ${$out_h_ref} sprintf("<TR>\n\t<TD>");
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319 my $win_start = min($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]) - $window;
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320 my $win_end = max($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]) + $window;
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321 print ${$out_h_ref} sprintf("<A HREF=\"http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s:%s-%s&display_app=ucsc&authz_method=display_at", $db, $interval_array_ref->[${$ichrom}], $win_start, $win_end);
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322 my $left_end = $interval_array_ref->[${$istart}];
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323 my $right_end = $interval_array_ref->[${$iend}];
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324 my $fstart_pos;
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325 my $fend_pos;
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326 if (defined($cturl)) {
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327 #print ${$out_h_ref} sprintf ("&hgt.customText=%s/display_as?id=%s&display_app=ucsc&authz_method=display_at", $server_url, $out_dbkey);
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328 print ${$out_h_ref} sprintf("&hgt.customText=%s", $cturl);
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329 }
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330 print ${$out_h_ref} sprintf("\">UCSC Visualization</A></TD><TD>");
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331 #custom track stuff something like : &hgt.customText=%s/display_as?id=%s&display_app=ucsc&authz_method=display_at, $server_url, $out_dbkey
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332 print ${$out_h_ref} join("</TD><TD>", @{$interval_array_ref});
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333 my @sorted_keys = sort {$a <=> $b} keys %{$result_hash_ref};
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334 if (defined($sorted_keys[0])) {
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335 foreach my $next_key (@sorted_keys) {
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336 foreach my $res (keys %{$result_hash_ref->{$next_key}}) {
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337 if (${$capture}) {
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338 if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '+') {
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339 $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}] - ${$promoter_len};
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340 } else {
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341 $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}];
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342 }
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343 if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '-') {
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344 $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}] + ${$promoter_len};
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345 } else {
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346 $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}];
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347 }
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348 if ($fstart_pos < $left_end) { $left_end = $fstart_pos; }
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349 if ($fend_pos > $right_end) { $right_end = $fend_pos; }
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350 }
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351
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352 if (!${$dd_ref}) {
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353 print ${$out_h_ref} sprintf("<TD>%s</TD>", $res);
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354 } else {
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355 if ($next_key == $ENCOMPASSING) {
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356 print ${$out_h_ref} sprintf("<TD>%s (%s)</TD>", $res, $ENCOMPASSING_STR);
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357 }
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358 elsif ($next_key == $INTERNAL) {
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359 print ${$out_h_ref} sprintf("<TD>%s (%s)</TD>", $res, $INTERNAL_STR);
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360 }
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361 else {
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362 print ${$out_h_ref} sprintf("<TD>%s (%s bp %s)</TD>", $res, $next_key, @{$result_hash_ref->{$next_key}->{$res}}[0]);
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363 }
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364 }
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365 }
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366 }
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367
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|
368 if (${$capture}) {
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369 print ${$out_h_ref} sprintf("<TD>%s</TD><TD>%s</TD><TD>%s</TD>", $left_end, $right_end, $right_end - $left_end);
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370 }
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371 }
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372 else {
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|
373 print ${$out_h_ref} sprintf("<TD>No results within $window bp window</TD>");
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|
374 }
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375 print ${$out_h_ref} sprintf("</TD>\n</TR>\n");
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|
376 }
|
