Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/calcolo_p_v4_norm_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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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
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2
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3 # Copyright 2009 Matteo Cesaroni, Lucilla Luzi
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4 #
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5 # This program is free software; ; you can redistribute it and/or modify
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6 # it under the terms of the GNU Lesser General Public License as published by
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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.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14
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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
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17 #prende tutte le probes che mecciano almeno in parte dentro gli esoni
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18
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19 use Statistics::PointEstimation;
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20 use Statistics::TTest;
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21 #use Statistics::Test::WilcoxonRankSum;
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22 use Getopt::Long;
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23
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24 GetOptions (
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25 "help" => \$OPT{help},
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26 "ann=s" => \$OPT{ann},
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27 "wt=s" => \$OPT{wt},
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28 "treat=s" => \$OPT{treat},
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29 "out=s" => \$OPT{out},
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30 "pv=s" => \$OPT{prob},
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31 "rc=s" => \$OPT{raw_cut},
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32 "fc=s" => \$OPT{fc_cut},
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33 "exon=s" => \$OPT{exon},
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34 "opt=s" => \$OPT{option},
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35 "norm=s" =>\$OPT{norm_q},
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36 "sum_met=s" =>\$OPT{sum_met},
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37 "fdr=s" =>\$OPT{fdr},
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38 "log=s" =>\$OPT{log_t},
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39 )|| printusage();
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40
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41 # opzioni da linea di comando
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42 my $file_ann=$OPT{ann};
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43 my $file_wt=$OPT{wt};
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44 my $file_treat=$OPT{treat};
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45 my $file_output=$OPT{out};
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46 my $pv_cut=$OPT{prob};
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47 my $media_cut=$OPT{raw_cut};
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48 my $FC_cut=$OPT{fc_cut};
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49 my $tipo=$OPT{exon};
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50 my $option=$OPT{option};
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51 my $normalization_q=$OPT{norm_q};
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52 my $sum_meth=$OPT{sum_met};
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53 my $corretction=$OPT{fdr};
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54 my $data_log=$OPT{log_t};
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55
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56 $help and printusage();
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57
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58
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59 if($option eq "comp"){
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60 if ($sum_meth eq "both"){
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61 $header=<<e0c6654;
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62 \# annotation_file: $file_ann
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63 \# wt_file: $file_wt
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64 \# treat_file: $file_treat
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65 \# p-value cutoff: $pv_cut
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66 \# raw data cutoff cutoff: $media_cut
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67 \# summary method: $sum_meth
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68 \# fold change cutoff: $FC_cut
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69 \# type of analysis: $tipo
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70 \# headers: name RefSeq Chr txStart txEnd strand mean_chip1 mean_chip2 FC_mean median_chip1 median_chip2 FC_median num_probes_in_gene p-value FDR(q-value)
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71 e0c6654
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72
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73 }
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74 if ($sum_meth eq "mean"){
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75 $header=<<e0c6654;
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76 \# annotation_file: $file_ann
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77 \# wt_file: $file_wt
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78 \# treat_file: $file_treat
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79 \# p-value cutoff: $pv_cut
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80 \# raw data cutoff cutoff: $media_cut
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81 \# summary method: $sum_meth
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82 \# fold change cutoff: $FC_cut
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83 \# type of analysis: $tipo
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84 \# headers: name RefSeq Chr txStart txEnd strand mean_chip1 mean_chip2 FC_mean num_probes_in_gene p-value FDR(q-value)
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85 e0c6654
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86
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87 }
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88 if ($sum_meth eq "median"){
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89 $header=<<e0c6654;
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90 \# annotation_file: $file_ann
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91 \# wt_file: $file_wt
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92 \# treat_file: $file_treat
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93 \# p-value cutoff: $pv_cut
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94 \# raw data cutoff cutoff: $media_cut
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95 \# summary method: $sum_meth
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96 \# fold change cutoff: $FC_cut
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97 \# type of analysis: $tipo
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98 \# headers: name RefSeq Chr txStart txEnd strand median_chip1 median_chip2 FC_median num_probes_in_gene p-value FDR(q-value)
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99 e0c6654
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100
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101 }
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102
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103
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104
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105 # "usage" se non ci sono opzioni
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106 if (!$file_ann || !$file_wt || !$file_treat) {
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107 &printusage()
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108 }
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109
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110 #if ($pv_cut == 1){$pv_cut=0.9999;}
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111 if (!$media_cut){$media_cut=0;}
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112 if (!$FC_cut){$FC_cut=0;}
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113
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114 my @r1=();
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115 my @r2=();
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116
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117 #my $confident=(1-$pv_cut)*100;
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118 #inserire nell'ordine: tabella annotazione, tabella valori wt, tabella valori treated, p-value cutoff, raw signal cutoff
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119
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120
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121 open (annotation,"<$file_ann") || die "file_ann not open:$!\n";
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122 open (wt,"<$file_wt") || die "$file_wt not open:$!\n";
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123 open (treated,"<$file_treat") || die "$file_treat not open:$!\n";
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124 open (output,">$file_output") || die "bed_$file_wt not open:$!\n";
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125
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126 print output "$header";
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127
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128 print "Comparison --> probe_selection=$tipo, Normalization=$normalization_q, summary method=$sum_meth Filters: p-value=$pv_cut, raw value=$media_cut, FC=$FC_cut";
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129
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130 while (defined (my $line_down = <annotation>)) {
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131 chomp $line_down;
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132 my @tmp_down = split("\t", $line_down);
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133 my @probe_match=split("\,", $tmp_down[9]);
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134 foreach $probes (@probe_match){
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135 my @coord=split("-", $probes);
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136 $tab_tot{$tmp_down[0]}{"$coord[0]\t$coord[1]"}.="$tmp_down[1]\n$tmp_down[7]\n$tmp_down[0]\n$tmp_down[2]\n$tmp_down[3]\n$tmp_down[4]\n$tmp_down[5]\n$tmp_down[6]\n";
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137 push(@ciclo,"$tmp_down[0]\t$coord[0]\t$coord[1]");
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138 }
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139 }
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140
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141 while (defined (my $line_down = <wt>)) {
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142 chomp $line_down;
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143 my @tmp_down = split("\t", $line_down);
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144 chomp $tmp_down[0];
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145 $tab_tot_wt{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
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146 }
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147
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148
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149 while (defined (my $line_down = <treated>)) {
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150 chomp $line_down;
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diff changeset
151 my @tmp_down = split("\t", $line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
152 chomp $tmp_down[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
153 $tab_tot_treat{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
154 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
155
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
156 if($normalization_q eq "yes"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
157
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
158 @sort_wt=sort{$tab_tot_wt{$a} <=> $tab_tot_wt{$b}} keys %tab_tot_wt;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
159 @sort_treat=sort{$tab_tot_treat{$a} <=> $tab_tot_treat{$b}} (keys %tab_tot_treat);
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 for($i=0;$i<=$#sort_wt;$i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
162 $media=($tab_tot_wt{$sort_wt[$i]}+$tab_tot_treat{$sort_treat[$i]})/2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
163 $tab_tot_value{$sort_wt[$i]}.="$media\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
164 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
165
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
166 for($i=0;$i<=$#sort_treat;$i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
167 $media=($tab_tot_wt{$sort_wt[$i]}+$tab_tot_treat{$sort_treat[$i]})/2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
168 $tab_tot_value{$sort_treat[$i]}.="$media\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
171 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
172
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
173
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
174 foreach $key_value(@ciclo){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
175
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
176 @keys_values=split("\t",$key_value);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
177 @array1= split("\n",$tab_tot{$keys_values[0]}{"$keys_values[1]\t$keys_values[2]"});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
178 if($normalization_q eq "yes"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
179 @array2= split("\n",$tab_tot_value{"$keys_values[1]\t$keys_values[2]"});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
180 $value1=$array2[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
181 $value2=$array2[1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
182 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
183 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
184 $value1=$tab_tot_wt{"$keys_values[1]\t$keys_values[2]"};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
185 $value2=$tab_tot_treat{"$keys_values[1]\t$keys_values[2]"};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
186 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
187 if ($tipo eq "internal_exon"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
188 $prendo = "^exon";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
189 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
190 if ($tipo eq "all_exon"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
191 $prendo = "exon";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
192 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
193 if ($tipo eq "last_exon"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
194 $prendo = "exon last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
195 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
196
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
197 if ((!($array1[0] eq "")) && ($array1[1] =~ /$prendo/g)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
198 if ($data_log eq "no_log"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
199 $log1=log($value1)/log(2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
200 $log2=log($value2)/log(2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
201 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
202 if ($data_log eq "log"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
203 $log1=$value1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
204 $log2=$value2;
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 $tab_gene_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
207 $tab_gene_tratted{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log2\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
208 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
209
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
210 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
211
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
212 foreach $key (keys %tab_gene_wt) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
213 @r1=split("\n",$tab_gene_wt{$key});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
214 @r2=split("\n",$tab_gene_tratted{$key});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
215
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
216 sort {$a <=> $b} (@r1);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
217 sort {$a <=> $b} (@r2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
218
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
219 if ($#r1>0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
220 my $ttest = new Statistics::TTest;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
221 $ttest->set_significance(95);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
222 $ttest->load_data(\@r1,\@r2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
223 my $s1=$ttest->{s1};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
224 my $s2=$ttest->{s2};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
225 $media1=$s1->{mean};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
226 $media2=$s2->{mean};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
227 $total_probes=$#r1+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
228 $potenza_a=$media2-$media1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
229 $FCa=((2)**$potenza_a);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
230 if( (@r1 % 2) == 1 ) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
231 $median1 = $r1[((@r1+1) / 2)-1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
232 $median2 = $r2[((@r2+1) / 2)-1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
233 } else {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
234 $median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
235 $median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
236 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
237 $potenza_m=$median2-$median1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
238 $FCm=((2)**$potenza_m);
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 ($FCa<1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
242 $FCa=(-(1/$FCa));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
243 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
244
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 if ($FCm<1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
247 $FCm=(-(1/$FCm));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
248 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
249 if ($sum_meth eq "mean"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
250 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCa))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
251 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
252 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
253 $p_value{"$key\t$media1\t$media2\t$FCa\t$total_probes"}=$ttest->{t_prob};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
254
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
255 #print output "$key\t$media1\t$media2\t$FCa\t",$ttest->{t_prob},"\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
256 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
257 if ($sum_meth eq "median"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
258 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCm))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
259 next;
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 #print output "$key\t$median1\t$median2\t$FCm\t",$ttest->{t_prob},"\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
262 $p_value{"$key\t$median1\t$median2\t$FCm\t$total_probes"}=$ttest->{t_prob};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
263 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
264 if ($sum_meth eq "both"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
265 if (($media1<$media_cut) && ($media2<$media_cut)){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
266 next;
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 #print output "$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t",$ttest->{t_prob},"\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
269 $p_value{"$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t$total_probes"}=$ttest->{t_prob};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
270 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
271 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
272 if ($#r1==0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
273 $media1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
274 $media2=$r2[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
275 $median1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
276 $median2=$r2[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
277 $potenza=$media2-$media1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
278 $FCa=((2)**$potenza);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
279 $FCm=((2)**$potenza);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
280 if ($FCa<1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
281 $FCa=(-(1/$FCa));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
282 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
283 if ($FCm<1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
284 $FCm=(-(1/$FCm));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
285 }
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 ($sum_meth eq "both"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
288 if (($media1<$media_cut) && ($media2<$media_cut)){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
289 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
290 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
291 $p_value{"$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t$total_probes"}=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
292 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
293 if ($sum_meth eq "mean"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
294 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCa))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
295 next;
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 $p_value{"$key\t$media1\t$media2\t$FCa\t$total_probes"}=1;
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 if ($sum_meth eq "median"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
300 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCm))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
301 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
302 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
303 $p_value{"$key\t$median1\t$median2\t$FCm\t$total_probes"}=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
304 }
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 }
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 @sort_pvalue=sort{$p_value{$a} <=> $p_value{$b}} keys %p_value;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
309
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
310 if($corretction eq "yes"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
311 for($i=0;$i<=$#sort_pvalue;$i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
312 $qvalue=$p_value{$sort_pvalue[$i]}*(($#sort_pvalue+1)/($i+1));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
313 push(@QVALUE, $qvalue);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
314 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
315
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
316 @qvalue_sort = sort {$a <=> $b} @QVALUE;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
317
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
318 for($i=0;$i<=$#sort_pvalue;$i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
319 #$FDR=((($i+1)*0.05)/($#sort_pvalue+1));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
320 $qvalue=shift(@qvalue_sort);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
321 if($qvalue>1){$qvalue=1;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
322 if($pv_cut>=$qvalue){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
323 print output "$sort_pvalue[$i]\t$p_value{$sort_pvalue[$i]}\t$qvalue\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
324 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
325 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
326 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
327 if($corretction eq "no"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
328 for($i=0;$i<=$#sort_pvalue;$i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
329 if($pv_cut>=$qvalue){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
330 print output "$sort_pvalue[$i]\t$p_value{$sort_pvalue[$i]}\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
331 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
332 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
333 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
334
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
335
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
336
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
337
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
338
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
339 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
340 if($option eq "expr"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
341 if ($sum_meth eq "median"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
342 $header=<<e0c6654;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
343 \# annotation_file: $file_ann
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
344 \# expression_file: $file_wt
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
345 \# type of analysis: $tipo
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
346 \# summary method: $sum_meth
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
347 \# headers: name RefSeq Chr txStart txEnd strand median_chip num_probes_in_gene
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
348 e0c6654
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
349
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
350 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
351 if ($sum_meth eq "mean"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
352 $header=<<e0c6654;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
353 \# annotation_file: $file_ann
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
354 \# expression_file: $file_wt
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
355 \# type of analysis: $tipo
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
356 \# summary method: $sum_meth
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
357 \# headers: name RefSeq Chr txStart txEnd strand mean_chip num_probes_in_gene
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
358 e0c6654
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
359
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
360 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
361 if ($sum_meth eq "both"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
362 $header=<<e0c6654;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
363 \# annotation_file: $file_ann
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
364 \# expression_file: $file_wt
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
365 \# type of analysis: $tipo
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
366 \# summary method: $sum_meth
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
367 \# headers: name RefSeq Chr txStart txEnd strand mean_chip median_chip num_probes_in_gene
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
368 e0c6654
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
369
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
370 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
371 if (!$file_ann || !$file_wt) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
372 &printusage()
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
373 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
374 my @r1=();
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
375 my @r2=();
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
376
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
377
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
378 open (annotation,"<$file_ann") || die "file_ann not open:$!\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
379 open (wt,"<$file_wt") || die "$file_wt not open:$!\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
380 open (output,">$file_output") || die "bed_$file_wt not open:$!\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
381
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
382 print output "$header";
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 print "Expression --> probe_selection=$tipo summary method=$sum_meth";
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 while (defined (my $line_down = <annotation>)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
387 chomp $line_down;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
388 my @tmp_down = split("\t", $line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
389 my @probe_match=split("\,", $tmp_down[9]);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
390 foreach $probes (@probe_match){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
391 my @coord=split("-", $probes);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
392 $tab_tot{$tmp_down[0]}{"$coord[0]\t$coord[1]"}.="$tmp_down[1]\n$tmp_down[7]\n$tmp_down[0]\n$tmp_down[2]\n$tmp_down[3]\n$tmp_down[4]\n$tmp_down[5]\n$tmp_down[6]\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
393 push(@ciclo,"$tmp_down[0]\t$coord[0]\t$coord[1]");
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 while (defined (my $line_down = <wt>)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
398 chomp $line_down;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
399 $line_down=~ s/ //g;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
400 my @tmp_down = split("\t", $line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
401 chomp $tmp_down[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
402 $tab_tot_wt{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
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 #@sort_wt=sort{$tab_tot_wt{$a} <=> $tab_tot_wt{$b}} keys %tab_tot_wt;
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 #print "ciclo = $ciclo[0]\t$ciclo[1]\n";
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 foreach $key_value(@ciclo){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
410
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
411 @keys_values=split("\t",$key_value);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
412 @array1= split("\n",$tab_tot{$keys_values[0]}{"$keys_values[1]\t$keys_values[2]"});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
413 @array2= split("\n",$tab_tot_wt{"$keys_values[1]\t$keys_values[2]"});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
414
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
415 if ($tipo eq "internal_exon"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
416 $prendo = "^exon";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
417 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
418 if ($tipo eq "all_exon"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
419 $prendo = "exon";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
420 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
421 if ($tipo eq "last_exon"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
422 $prendo = "exon last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
423 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
424
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
425 if ((!($array1[0] eq "")) && ($array1[1] =~ /$prendo/g)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
426
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
427 if ($data_log eq "no_log"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
428 $log1=log($array2[0])/log(2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
429 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
430 if ($data_log eq "log"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
431 $log1=$array2[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
432 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
433
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
434 $tab_gene_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
435 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
436 if ((!($array1[0] eq "")) && ($array1[1] =~ /intron/g)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
437 if ($data_log eq "no_log"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
438 $log1=log($array2[0])/log(2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
439 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
440 if ($data_log eq "log"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
441 $log1=$array2[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
442 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
443 $tab_intron_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
444 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
445
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
446 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
447
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
448
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
449 foreach $key (keys %tab_gene_wt) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
450 @r1=split("\n",$tab_gene_wt{$key});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
451 if (exists $tab_intron_wt{$key}){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
452 @r2=split("\n",$tab_intron_wt{$key});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
453 sort {$a <=> $b} (@r2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
454 }else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
455 @r2=("no");
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
456 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
457 sort {$a <=> $b} (@r1);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
458 if ($#r2>0) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
459 if ($#r1>0) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
460 my $ttest = new Statistics::TTest;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
461 $ttest->set_significance(95);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
462 $ttest->load_data(\@r1,\@r2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
463 my $s1=$ttest->{s1};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
464 my $s2=$ttest->{s2};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
465 $media1=$s1->{mean};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
466 $media2=$s2->{mean};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
467 $total_probes=$#r1+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
468 $total_probes2=$#r2+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
469 if( (@r1 % 2) == 1 ) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
470 $median1 = $r1[((@r1+1) / 2)-1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
471 } else {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
472 $median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
473 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
474 if( (@r2 % 2) == 1 ) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
475 $median2 = $r2[((@r2+1) / 2)-1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
476 } else {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
477 $median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
478 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
479 if($media1>=$media2){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
480 $pvalue=$ttest->{t_prob};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
481 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
482 if($media1<$media2){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
483 $pvalue=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
484 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
485 if ($sum_meth eq "mean"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
486 print output "$key\t$media1\t$media2\t$pvalue\t$total_probes\t$total_probes2\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
487 #print output "$key\t$media1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
488 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
489 if ($sum_meth eq "median"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
490 print output "$key\t$median1\t$median2\t$pvalue\t$total_probes\t$total_probes2\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
491 #print output "$key\t$median1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
492 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
493 if ($sum_meth eq "both"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
494 print output "$key\t$media1\t$media2\t$median1\t$median2\t$pvalue\t$total_probes\t$total_probes2\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
495 #print output "$key\t$media1\t$median1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
496 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
497 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
498 if ($#r1==0) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
499 @r1=@r2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
500 my $ttest = new Statistics::TTest;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
501 $ttest->set_significance(95);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
502 $ttest->load_data(\@r1,\@r2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
503 my $s2=$ttest->{s2};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
504 $media2=$s2->{mean};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
505 $total_probes=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
506 $total_probes2=$#r2+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
507 $media1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
508 $median1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
509 if( (@r2 % 2) == 1 ) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
510 $median2 = $r2[((@r2+1) / 2)-1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
511 } else {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
512 $median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
513 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
514 if ($sum_meth eq "mean"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
515 print output "$key\t$media1\t$media2\tNA\t$total_probes\t$total_probes2\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
516 #print output "$key\t$media1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
517 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
518 if ($sum_meth eq "median"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
519 print output "$key\t$median1\t$median2\tNA\t$total_probes\t$total_probes2\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
520 #print output "$key\t$median1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
521 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
522 if ($sum_meth eq "both"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
523 print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t$total_probes\t$total_probes2\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
524 #print output "$key\t$media1\t$median1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
525 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
526 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
527
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
528
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
529 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
530
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
531 if ($r2[0] eq "no") {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
532 if ($#r1>0) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
533 @r2=@r1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
534 my $ttest = new Statistics::TTest;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
535 $ttest->set_significance(95);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
536 $ttest->load_data(\@r1,\@r2);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
537 my $s1=$ttest->{s1};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
538 $media1=$s1->{mean};
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
539 $total_probes=$#r1+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
540 if( (@r1 % 2) == 1 ) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
541 $median1 = $r1[((@r1+1) / 2)-1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
542 } else {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
543 $median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
544 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
545 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
546 if ($#r==0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
547 $media1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
548 $median1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
549 $total_probes=$#r1+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
550 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
551 $media2=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
552 $median2=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
553 if ($sum_meth eq "both"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
554 print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t$total_probes\t0\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
555 #print output "$key\t$media1\t$median1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
556 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
557 if ($sum_meth eq "mean"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
558 print output "$key\t$media1\t$media2\tNA\t$total_probes\t0\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
559 #print output "$key\t$media1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
560 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
561 if ($sum_meth eq "median"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
562 print output "$key\t$median1\t$median2\tNA\t$total_probes\t0\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
563 #print output "$key\t$median1\t$total_probes\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
564 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
565 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
566 if (($#r2 == 0) && ($r2[0] ne "no") && ($#r1==0)){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
567 $media1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
568 $media2=$r2[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
569 $median1=$r1[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
570 $median2=$r2[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
571 if ($sum_meth eq "both"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
572 print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t1\t1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
573 #print output "$key\t$media1\t$median1\t1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
574 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
575 if ($sum_meth eq "mean"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
576 print output "$key\t$media1\t$media2\tNA\t1\t1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
577 #print output "$key\t$media1\t1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
578 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
579 if ($sum_meth eq "median"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
580 print output "$key\t$median1\t$median2\tNA\t1\t1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
581 #print output "$key\t$median1\t1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
582 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
583 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
584 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
585
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
586
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
587
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
588
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
589 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
590
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
591
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
592
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
593
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
594
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
595 ####################################################################################################################################
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
596
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
597 sub printusage {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
598
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
599 print<<eoc22334;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
600
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
601
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
602
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
603 ***************************************************************
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
604 :: N i m b l e G e n E x p r e s s i o n A n a l y s i s ::
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
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605 ***************************************************************
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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606
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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607
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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608 USAGE SUMMARY
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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609 ---------------------------------------------------------------------------------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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610 This program utilizes NimbleGen ratio files in gff format as INPUT FILE and
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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611 provides a table of the computed picks in the same gff file format.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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612
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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613
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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614 --ann annotation file
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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615 --wt wild type file
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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616 --treat treated file
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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617 --pv p-value cut-off
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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618 --rc raw signal cut-off
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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619 --fc fold change cut-toff
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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620
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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621 -----------------------------------------------------------------------------------------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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622 EXAMPLES:
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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623
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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624 perl program.pl --in 75340_ratio.gff --perc 0.98 --t s --num 3 --dist 250 --w 500
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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625 OR
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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626 perl program.pl --in 75340_ratio.gff --perc 0.98 --t p --log 5 --num 3 --dist 250 --w 500
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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627
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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628 -----------------------------------------------------------------------------------------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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629
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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630 eoc22334
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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631 exit 0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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632
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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633 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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634
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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635
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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636