Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/MapToExon_RefSeqMat_new.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
parents
children 78770028dcf1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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 #
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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5 # 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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6 # 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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7 # 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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8 # 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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9 #
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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10 # 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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11 # 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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12 # 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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13 # 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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14
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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15
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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16 $|=1;
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17 my $infile = $ARGV[0];
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18 my $infile2=$ARGV[1];
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19 my $definition_pro=$ARGV[2];
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20 my $definition_tre=$ARGV[3];
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21 my $priority=$ARGV[4];
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22 my $file_output=$ARGV[5];
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23
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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24 open (INFILE, "<$infile");
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25 open (INFILE2, "<$infile2");
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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26 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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27
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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28 $campi_t=0;
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29 $definition_out=$definition_pro-2000;
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30
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31 while (defined (my $line_down = <INFILE2>)) {
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32 $line_down=~ s/\#//g;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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33 chomp($line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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34 $campi_t++;
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35 my @tmp_down=split(/\s+/, $line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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36 if($campi_t==1){
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37 $z=0;
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38 foreach $campo_t(@tmp_down){
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39 if(($campo_t eq "name") || ($campo_t eq "qName") || ($campo_t eq "repClass")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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40 $zRef=$z;
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41 }
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42 if(($campo_t eq "txStart") || ($campo_t eq "tStart") || ($campo_t eq "chromStart")|| ($campo_t eq "genoStart")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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43 $ztxStart=$z;
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44 }
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45 if(($campo_t eq "txEnd") || ($campo_t eq "tEnd") || ($campo_t eq "chromEnd")|| ($campo_t eq "genoEnd")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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46 $ztxEnd=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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47 }
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48 if($campo_t eq "strand"){
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49 $zstrand=$z;
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50 }
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51 if(($campo_t eq "chrom") || ($campo_t eq "tName")|| ($campo_t eq "genoName")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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52 $zchrom=$z;
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53 }
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54 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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55 $zexonstart=$z;
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56 }
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57 if($campo_t eq "exonEnds"){
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58 $zexonend=$z;
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59 }
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60 if($campo_t eq "blockSizes"){
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61 $zblocksize=$z;
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62 }
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63 if(($campo_t eq "name2") || ($campo_t eq "repFamily")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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64 $zname=$z;
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65 }
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66 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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67 $zcount=$z;
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68 }
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69 $z++;
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70 }
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71 if(!$zname){
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72 $zname=$zRef;
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73 }
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74 if(!$zexonstart){
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75 $zexonstart=$ztxStart;
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76 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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77 if(!$zexonend){
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78 $zexonend=$ztxEnd;
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79 }
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80 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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81 print "Annotation file is not in the accepted format\n";
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82 exit;
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83 }else{print "promoter=$definition_pro, priority=$priority";}
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84 next;
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85 }
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86 chomp $tmp_down[$zchrom];
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87 $tab_ann{$tmp_down[$zchrom]}.="$line_down\n";
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88 }
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89
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90 while (defined (my $line_down = <INFILE>)) {
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91 my @tmp_down = split("\t", $line_down);
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92 chomp $tmp_down[0];
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93 $tab_probe{$tmp_down[0]}.=$line_down;
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94 }
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95
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96 @chrom_probes= keys(%tab_probe);
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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 &chip;
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99
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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100 exit 0;
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101
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102 ###########
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103 #subrutine#
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104 ###########
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105
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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106 sub chip
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107 {
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108 foreach $chromosoma (@chrom_probes){
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109
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110 @file1=split("\n", $tab_probe{$chromosoma});
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111
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112 foreach $line(@file1) {
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113 chomp $line;
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114 #chop $line;
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115 if ($line=~/track/g){next;}
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116 if ($line=~/#/g){next;}
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117 if ($line=~/^\s+$/g){next;}
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118 my @Line=split(/\t/, $line);
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119 my $Chrom=$Line[0];
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120 my $Start=$Line[3];
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121 my $Stop=$Line[4];
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122 #my $value=$Line[5];
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123 my $ProbeName=$Line[5];
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124 my $feature="ciccio";
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125 my $check=0;
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126 my $relative_dist=10000000;
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127 $double_check=0;
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128 @file2=split("\n", $tab_ann{$chromosoma});
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129 foreach $linea(@file2) {
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130 chomp $linea;
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131 $linea=~ s/\#//g;
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132 my @kEle=split("\t", $linea);
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133 $ref=$kEle[$zRef];
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134 $chrom=$kEle[$zchrom];
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135 $strand=$kEle[$zstrand];
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136 $transcriptStart=$kEle[$ztxStart];
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137 $transcriptStop=$kEle[$ztxEnd];
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138 if($zcount){
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139 $exoncount=$kEle[$zcount];
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140 }
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141 else
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142 {
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143 $exoncount=1;
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144 }
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145 $geneName=$kEle[$zname];
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146 $exonStartref=$kEle[$zexonstart];
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147 my $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand";
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148
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149 my @exonStart=split(",", $exonStartref);
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150
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151 if (!$zblocksize){
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152 $exonEndref=$kEle[$zexonend];
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153 }
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154 else {
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diff changeset
155 @blockStop=split(",", $kEle[$zblocksize]);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
156 $exonEndref="";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
157 for ($jj=0; $jj<=$#exonStart; $jj++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
158 $end_block=$exonStart[$jj]+$blockStop[$jj];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
159 $exonEndref.="$end_block,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
160
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
161 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
162 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
163
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
164 my @exonStop=split(",", $exonEndref);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
165
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
166 #print "$ref / $chrom / $strand / $transcriptStart/$transcriptStop/$exoncount/$geneName [$#exonStop]\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
167 #print "pippo $exonStart[0] - $exonStop[0],$exonStart[1] - $exonStop[1],$exonStart[2] - $exonStop[2] \n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
168
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
169
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
170 if ($Chrom eq $chrom) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
171 #print "cazzo";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
172 if ($strand eq "+"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
173 $promotore=$transcriptStart+$definition_pro;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
174 $distanzaTSS=int((($Start+$Stop)/2)-$transcriptStart);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
175 $trepr=$transcriptStop+$definition_tre;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
176 $rel_start=$promotore;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
177 $rel_stop=$trepr;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
178 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
179 if ($strand eq "-"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
180 $promotore=$transcriptStop-$definition_pro;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
181 $distanzaTSS=int($transcriptStop-(($Start+$Stop)/2));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
182 $trepr=$transcriptStart-$definition_tre;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
183 $rel_start=$trepr;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
184 $rel_stop=$promotore;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
185 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
186 #print OUTFILE1 "$ref\t$distanzaTSS\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
187
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
188 #if(($Start<=$transcriptStart && $Stop>$transcriptStart) || ($Start>=$promotore && $Stop<=$transcriptStart) || ($Start>=$transcriptStop && $Stop<=$promotore) || ($Start<=$promotore && $Stop>$promotore) || ($Start<$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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parents:
diff changeset
189 #print "sono entrato con start $Start stop $Stop e $transcriptStart e $transcriptStop\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
190
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
191 if($Start<=$rel_stop && $rel_start<=$Stop){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
192
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
193 for(my $i=0;$i<=$#exonStart;$i++) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
194
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
195 if ($strand eq "+"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
196 $exoncount1=$i+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
197 $exoncount2=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
198 $introncount=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
199 if($i==$#exonStart) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
200 $exoncount2="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
201 $introncount="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
202 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
203 if($i==$#exonStart-1) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
204 $introncount="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
205 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
206 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
207 if ($strand eq "-"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
208 $exoncount1=($#exonStart+1)-$i;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
209 $exoncount2=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
210 $introncount=$exoncount1-1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
211 #if(($i==0) && ($#exonStart != 0)) {$exoncount2="last";}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
212 if($i==0) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
213 $exoncount2="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
214 $introncount="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
215 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
216 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
217 #print "esone start $exonStart[$i] e $exonStop[$i] e start $Start\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
218
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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parents:
diff changeset
219 #print OUTFILE1 "$ref\t$exonStart[$i]\t$exonStop[$i]\t$Start\t$Stop\t$i\t$#exonStart\t$priority\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
220
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
221
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
222
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
223 #if($priority eq "prom" && $check==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
224 # last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
225 #}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
226 #if($priority eq "gene" && $check==2){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
227 # next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
228 #}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
229
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
230
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
231 if(($Start<=$exonStart[$i]) && ($Stop>$exonStart[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
232 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tintronexon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
233 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
234 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
235 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
236 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
237 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
238 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
239 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
240 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
241 if(($Start>=$exonStart[$i]) && ($Stop<=$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
242 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\texon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
243 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
244 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
245 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
246 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
247 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
248 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
249 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
250 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
251 if(($Start<$exonStop[$i]) && ($Stop>$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
252 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\texonintron $introncount\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
253 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
254 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
255 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
256 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
257 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
258 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
259 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
260 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
261 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
262 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
matces
parents:
diff changeset
263 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tintron $introncount\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
264 #print "intron\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
265 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
266 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
267 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
268 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
269 if(($Start>=$exonStop[$i]) && ($Stop<=$exonStart[$i+1])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
270 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tintron $introncount\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
271 #print "intron\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
272 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
273 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
274 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
275
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
276
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
277
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
278 if (($strand eq "+") && ($Start>=$transcriptStop)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
279 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\t3_prime\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
280 $distanzaTSS=int($transcriptStop-(($Start+$Stop)/2));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
281 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
282 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
283 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
284 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
285 else{$check=1;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
286 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
287 if (($strand eq "-") && ($Stop<=$transcriptStart)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
288 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\t3_prime\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
289 $distanzaTSS=int((($Start+$Stop)/2)-$transcriptStart);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
290 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
291 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
292 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
293 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
294 else{$check=1;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
295 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
296
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
297
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
298
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
299
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
300 if (($strand eq "+") && (($Start<=$promotore && $Stop>$promotore) || ($Start>$promotore && $Stop<=$transcriptStart))) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
301 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tpromoter\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
302 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
303 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
304 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
305 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
306 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
307 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
308 if (($strand eq "-") && (($Start<=$promotore && $Stop>=$promotore) || ($Start>=$transcriptStop && $Stop<$promotore))) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
309 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tpromoter\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
310 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
311 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
312 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
313 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
314 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
315 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
316
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
317 if(($Start<=$exonStart[$i]) && ($i==0) && ($strand eq "+") && ($Stop>=$exonStart[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
318 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tprom_exon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
319 #print "prom-exon e $exoncount1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
320 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
321 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
322 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
323 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
324 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
325 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
326 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
matces
parents:
diff changeset
327 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tprom_exon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
328 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
329 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
330 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
331 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
332 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
333 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
334
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
335 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
336 #if ($check==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
337 # print "$chrom\t$Start\t$Stop\t$geneName\t$exoncount\t$ref\t$strand\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
338 #}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
339 }else{next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
340 #exit;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
341 }else{next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
342
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
343 #print OUTFILE1 "$ref\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
344 #print "$geneName\t$transcriptStart\t$Chrom\t$Start\t$Stop\t$distanzaTSS\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
345
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
346 if (($priority eq "gene") && ($relative_dist>abs($distanzaTSS))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
347 $relative_dist=abs($distanzaTSS);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
348 $stampa="$Chrom\t$Start\t$Stop\t$ProbeName\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
349 $double_check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
350 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
351 if (($check==1) && ($priority eq "prom") && ($relative_dist>abs($distanzaTSS))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
352 $relative_dist=abs($distanzaTSS);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
353 $double_check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
354 $stampa="$Chrom\t$Start\t$Stop\t$ProbeName\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
355 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
356 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
357
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
358
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
359
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
360 if($double_check==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
361 print OUTFILE1 "$stampa";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
362 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
363 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
364 if (($check==2) && ($priority eq "prom")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
365 print OUTFILE1 "$Chrom\t$Start\t$Stop\t$ProbeName\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
366 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
367 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
368 if($check==0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
369 print OUTFILE1 "$Chrom\t$Start\t$Stop\t$ProbeName\tintergenic\tintergenic\t$Start\t$Stop\t+\t0\tOUT\t$definition_out\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
370 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
371 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
372 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
373 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
374 close INFILE;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
375 close INFILE2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
376 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
377
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
378
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
379
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
380
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
381
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
382
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
383
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
384
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
385
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
386
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
387
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
388
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
389
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
390
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
391
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
392
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
393
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
394
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
395
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
396
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
397
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
398
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
399
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
400
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
401
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
402
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
403
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
404
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
405
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
406
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
407
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
408
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
409
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
410
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
411
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
412