Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/genecentrico.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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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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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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16 $file_all=$ARGV[0];
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17 $file_sub=$ARGV[1];
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18 $down=$ARGV[2];
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19 $up=$ARGV[6];
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20 $scelta=$ARGV[3];
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21 $result=$ARGV[4];
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22 $output=$ARGV[5];
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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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25 open(FILESUB, "<$file_sub") or die "Cannot find file $file_sub\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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26 open(FILEALL, "<$file_all") or die "Cannot open file $file_all: $!\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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27 open(FILEOUT, ">$output") or die "Cannot create file $output: $!\n";
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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29 print "Analysis Type=$scelta, Promoter def:$down/$up, output=$result\n";
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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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31 @sub=<FILESUB>;
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32 @all=<FILEALL>;
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33 foreach $lines_all(@all){
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34 chomp $lines_all;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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35 #chop $lines_all;
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36 if ($lines_all=~/#/g){next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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37 @line_all=split("\t",$lines_all);
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38 $chr=$line_all[2];
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39 $refseq=$line_all[1];
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40 $refStart=$line_all[3];
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41 $refStop=$line_all[4];
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42 $name=$line_all[0];
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43 #$exon_count=$line_all[8];
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44 #@exonStart=split(",",$line_all[9]);
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45 #@exonStop=split(",",$line_all[10]);
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46 $strand=$line_all[5];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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47 if ($scelta eq "promoter"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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48 if ($strand eq "+"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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49 $prom_start=$refStart+$down;
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50 $prom_stop=$refStart+$up;
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51 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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52 if ($strand eq "-"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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53 $prom_start=$refStop-$up;
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54 $prom_stop=$refStop-$down;
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55 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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56 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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57 if ($scelta eq "all"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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58 if ($strand eq "+"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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59 $prom_start=$refStart+$down;
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60 $prom_stop=$refStop;
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61 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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62 if ($strand eq "-"){
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63 $prom_start=$refStart;
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64 $prom_stop=$refStop-$down;
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65 }
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66 }
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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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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70 @promotore=();
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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71 $max_prom=0;
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72 foreach $lines_sub(@sub){
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73 chomp $lines_sub;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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74 if ($lines_sub=~/#/g){next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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75 @line_sub=split("\t",$lines_sub);
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76 $chr_p=$line_sub[0];
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77 $peakStart=$line_sub[3];
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78 $peakStop=$line_sub[4];
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79 $value=$line_sub[5];
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80 #print "$peakStart\t$peakStop\t$prom_start\t$prom_stop\n";
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81 #print "$refStart\t$refStop\t$peakStart\t$peakStop\n";
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82 if (((($peakStart>=$prom_start) && ($peakStart<=$prom_stop)) || (($peakStart<=$prom_start) && ($peakStop>=$prom_start))) && ("$chr" eq "$chr_p")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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83 push(@promotore,$value);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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84 #print "cazzo";
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85
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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86 }
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87 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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88 $i=0;
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89 foreach $valore(@promotore){
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90 $i++;
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91 if($max_prom<$valore){
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92 $max_prom=$valore;
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93 }
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94 }
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95 if ($result eq "max_value"){
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96 print FILEOUT "$lines_all\t$max_prom\n";
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97 }
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98 else{
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99 print FILEOUT "$lines_all\t$i\n";
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100 }
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101 }