Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/annotation_expr_intron.pl @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #!/usr/bin/perl
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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2
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 # Copyright 2009 Matteo Cesaroni, Lucilla Luzi
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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4 #
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5
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 # This program is free software; ; you can redistribute it and/or modify
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 # it under the terms of the GNU Lesser General Public License as published by
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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8 # the Free Software Foundation; either version 3 of the License, or (at your
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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9 # option) any later version.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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10 #
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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11 # This program is distributed in the hope that it will be useful,
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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14 # GNU General Public License for more details.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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17
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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18 $|=1;
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19 my $infile = $ARGV[0];
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20 my $infile2=$ARGV[1];
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21 my $file_output=$ARGV[2];
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22
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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23 open (INFILE, "<$infile");
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24 open (INFILE2, "<$infile2");
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25 open (OUTFILE1, ">$file_output") or die "Cannot find file $file_output\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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26
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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27 $campi_t=0;
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28 while (defined (my $line_down = <INFILE2>)) {
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29 $line_down=~ s/\#//g;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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30 chomp($line_down);
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31 $campi_t++;
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32 my @tmp_down=split(/\s+/, $line_down);
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33 if($campi_t==1){
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34 $z=0;
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35 foreach $campo_t(@tmp_down){
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36 if(($campo_t eq "name") || ($campo_t eq "qName")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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37 $zRef=$z;
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38 }
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39 if(($campo_t eq "txStart") || ($campo_t eq "tStart") || ($campo_t eq "chromStart")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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40 $ztxStart=$z;
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41 }
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42 if(($campo_t eq "txEnd") || ($campo_t eq "tEnd") || ($campo_t eq "chromEnd")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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43 $ztxEnd=$z;
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44 }
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45 if($campo_t eq "strand"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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46 $zstrand=$z;
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47 }
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48 if(($campo_t eq "chrom") || ($campo_t eq "tName")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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49 $zchrom=$z;
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50 }
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51 if(($campo_t eq "exonStarts") || ($campo_t eq "tStarts")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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52 $zexonstart=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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53 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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54 if($campo_t eq "exonEnds"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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55 $zexonend=$z;
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56 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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57 if($campo_t eq "blockSizes"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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58 $zblocksize=$z;
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59 }
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60 if($campo_t eq "name2"){
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61 $zname=$z;
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62 }
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63 if(($campo_t eq "exonCount")||($campo_t eq "blockCount")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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64 $zcount=$z;
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65 }
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66 $z++;
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67 }
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68 if(!$zname){
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69 $zname=$zRef;
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70 }
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71 if(!$zexonstart){
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72 $zexonstart=$ztxStart;
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73 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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74 if(!$zexonend){
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75 $zexonend=$ztxEnd;
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76 }
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77 if(($zRef eq "") || ($ztxStart eq "") || ($zstrand eq "") || ($zchrom eq "")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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78 print "Annotation file is not in the accepted format\n";
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79 exit;
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80 }else{print "Expression chip annotation";}
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81 next;
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82 }
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83 chomp $tmp_down[$zchrom];
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84 $tab_ann{$tmp_down[$zchrom]}.="$line_down\n";
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85 }
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86
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87 while (defined (my $line_down = <INFILE>)) {
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88 my @tmp_down = split("\t", $line_down);
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89 chomp $tmp_down[0];
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90 $tab_probe{$tmp_down[0]}.=$line_down;
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91 }
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92
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93 @chrom_probes= keys(%tab_probe);
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94
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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95 &expression;
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96
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97
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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98 exit 0;
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99
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100
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101 ###########
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102 #subrutine#
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103 ###########
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104
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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105 sub expression
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106 {
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107 foreach $chromosoma (@chrom_probes){
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108 %gene_cen="";
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109 @file2=split("\n", $tab_ann{$chromosoma});
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110 foreach $linea(@file2) {
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111 chomp $linea;
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112 $linea=~ s/#//g;
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113 my @kEle=split(/\s+/, $linea);
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114 $ref=$kEle[$zRef];
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115 $chrom=$kEle[$zchrom];
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116 $strand=$kEle[$zstrand];
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117 $transcriptStart=$kEle[$ztxStart];
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118 $transcriptStop=$kEle[$ztxEnd];
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119 if($zcount){
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120 $exoncount=$kEle[$zcount];
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121 }
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122 else
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123 {
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124 $exoncount=1;
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125 }
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126 $geneName=$kEle[$zname];
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127 $exonStartref=$kEle[$zexonstart];
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128
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129 my @exonStart=split(",", $exonStartref);
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130
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131 if (!$zblocksize){
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132 $exonEndref=$kEle[$zexonend];
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133 }
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134 else {
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135 @blockStop=split(",", $kEle[$zblocksize]);
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136 $exonEndref="";
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137 for ($jj=0; $jj<=$#exonStart; $jj++){
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138 $end_block=$exonStart[$jj]+$blockStop[$jj];
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139 $exonEndref.="$end_block,";
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140
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141 }
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142 }
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143
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144 my @exonStop=split(",", $exonEndref);
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145
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146 #print @exonStart;
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147
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148 @file1=split("\n",$tab_probe{$chromosoma});
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149
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150 foreach $line(@file1) {
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151 chomp $line;
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152 #chop $line;
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153 if ($line=~/track/g){next;}
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154 if ($line=~/#/g){next;}
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155 if ($line=~/^\s+$/g){next;}
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156 my @Line=split(/\t/, $line);
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157 my $Chrom=$Line[0];
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158 my $Start=$Line[3];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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159 my $Stop=$Line[4];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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160 my $ProbeName=$Line[5];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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161 my $feature="ciccio";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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162 if ($Chrom eq $chrom) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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163 if(($Start<=$transcriptStart && $Stop>$transcriptStart) || ($Start<$transcriptStop && $Stop>=$transcriptStop) || ($Start>=$transcriptStart && $Stop<=$transcriptStop) ){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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164 #print "sono entrato con start $Start stop $Stop e $transcriptStart e $transcriptStop\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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165
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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166 for($i=0;$i<=$#exonStart;$i++) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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167 if ($strand eq "+"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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168 $exoncount1=$i+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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169 $exoncount2=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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170 if($i==$#exonStart) {$exoncount2="last";}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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171 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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172 if ($strand eq "-"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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173 $exoncount1=($#exonStart+1)-$i;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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174 $exoncount2=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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175 if($i==0) {$exoncount2="last";}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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176 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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177
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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178 if(($Start<=$exonStart[$i]) && ($i==0) && ($strand eq "+")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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179 $feature="$chrom\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tprom_exon $exoncount2\t$exoncount1";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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180 $gene_cen{"$ref\t$geneName"}{$feature}.="$Chrom-$Start,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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181 last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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182 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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183 if(($Start<=$exonStop[$i]) && ($i==$#exonStart) && ($strand eq "-") && ($Stop>=$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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184 $feature="$chrom\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tprom_exon $exoncount2\t$exoncount1";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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185 $gene_cen{"$ref\t$geneName"}{$feature}.="$Chrom-$Start,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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186 last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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187 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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188 if(($Start<=$exonStart[$i]) && ($Stop>$exonStart[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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189 $feature="$chrom\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\t*intronexon $exoncount2\t$exoncount1";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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190 $gene_cen{"$ref\t$geneName"}{$feature}.="$Chrom-$Start,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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191 last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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192 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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193 if(($Start>=$exonStart[$i]) && ($Stop<=$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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194 $feature="$chrom\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\texon $exoncount2\t$exoncount1";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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195 $gene_cen{"$ref\t$geneName"}{$feature}.="$Chrom-$Start,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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196 last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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197 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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198 if(($Start<$exonStop[$i]) && ($Stop>$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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199 $feature="$chrom\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\t*exonintron $exoncount2\t$exoncount1";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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200 $gene_cen{"$ref\t$geneName"}{$feature}.="$Chrom-$Start,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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201 last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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202 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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203 if(($Start>=$exonStop[$i]) && ($Stop<=$exonStart[$i+1]) && ($check==0)){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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204 $feature="$chrom\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tintron $exoncount2\t$exoncount1";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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205 $gene_cen{"$ref\t$geneName"}{$feature}.="$Chrom-$Start,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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206 last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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207 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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208
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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209 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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210
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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211
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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212 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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213
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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214 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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215
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
216 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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217 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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218
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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219 foreach $nome (keys %gene_cen){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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220 foreach $description (keys %{$gene_cen {$nome}}) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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221 print OUTFILE1 "$nome\t$description\t$gene_cen{$nome}{$description}\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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222
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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223 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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224
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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225 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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226 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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227 close INFILE;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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228 close INFILE2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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229 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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230
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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231
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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232