Mercurial > repos > mir-bioinf > multi_join_left
annotate multi_join_left/addColumnsFromFile2ToFile1.pl @ 5:1de2a8f041b3 draft
Corrected xml syntax errors in config file, added missing pl script and output dataset to test-data
author | mir-bioinf |
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date | Tue, 21 Apr 2015 16:20:03 -0400 |
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5
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1 #! /usr/bin/perl -w |
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2 #=============================================================================== |
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3 # |
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4 # FILENAME: addColumnsFromFile2ToFile1.pl |
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5 # |
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6 # USAGE: see -help |
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7 # |
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8 # DESCRIPTION: This program adds columns in File 2 to File 1, |
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9 # if there are correnponding entries in File 1 |
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10 # |
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11 # AUTHOR: Ron Stewart |
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12 # VERSION: 1.1 |
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13 # CREATED: 12/18/06 CDT |
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14 #=============================================================================== |
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15 |
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16 use lib '/opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased'; ##CMS ADDED 11-05-14, DIR CONTAINS CUSTOM MODULE |
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17 |
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18 use strict; |
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19 use IO::File; |
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20 use GetOptWC; |
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21 # parsing the command line |
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22 my %optVarsIn = (); |
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23 # help information |
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24 $optVarsIn{'File1'} = './File1.txt`=s`Input file of genes to include'; |
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25 $optVarsIn{'File2'} = './File2.txt`=s`Input file to be added'; |
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26 $optVarsIn{'cola1'} = '2`=f`first column to look for match in File1'; |
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27 $optVarsIn{'colb1'} = '4`=f`second column to look for match in File1'; |
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28 $optVarsIn{'cola2'} = '2`=f`first column to look for match in File2'; |
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29 $optVarsIn{'colb2'} = '4`=f`second column to look for match in File2'; |
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30 $optVarsIn{'file1FirstColToCopy'} = '-1`=f`first column to copy in File1'; |
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31 $optVarsIn{'file1LastColToCopy'} = '-1`=f`last column to copy in File1'; |
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32 $optVarsIn{'file2FirstColToCopy'} = '-1`=f`first column to copy in File2'; |
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33 $optVarsIn{'file2LastColToCopy'} = '-1`=f`last column to copy in File2'; |
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34 $optVarsIn{'HelpPrefix'} = 'This script is for adding entries in File2 to the corresponding entries in File1.'; |
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35 $optVarsIn{'HelpSuffix'} = 'example call: ./addColumnsFromFile2ToFile1.pl -File1=./esAndDiffMarkersWithSage20061211.txt -cola1=2 -calb1=4 -File2=./pan_whole_table_fold_ann.txt -cola2=1 -colb2=4`Note: Two input files should have title lines`NOTE:Files must be text files, NOT .xls files. If you have an .xls file, save it as "Text(Windows) in Excel.'; |
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36 my %retVars = (); |
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37 my $retVarsRef = GetOptWC::getOptions(\%optVarsIn); |
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38 %retVars = %$retVarsRef; |
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39 if ($retVars{'HelpCalled'}) { |
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40 print "exiting now, help called\n"; |
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41 exit; |
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42 } |
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43 my $File1 = $retVars{'File1'}; |
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44 my $FHFile1; |
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45 $FHFile1 = IO::File->new("<$File1"); |
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46 |
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47 my $File2 = $retVars{'File2'}; |
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48 my $FHFile2; |
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49 $FHFile2 = IO::File->new("<$File2"); |
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50 my $File1name = $File1; |
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51 print "file1name: $File1name\n"; |
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52 $File1name =~ s/[\.\/]/_/g; |
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53 print "file1name: $File1name\n"; |
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54 |
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55 my $File2name = $File2; |
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56 $File2name =~ s/[\.\/]/_/g; |
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57 #my $Out = $File1name.'.'.$File2name; # this can be too long in some cases |
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58 my $Out = "file1_file2.txt"; |
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59 print" out is $Out\n"; |
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60 my $OutFile = IO::File->new(">$Out"); |
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61 my $cola1 = $retVars{'cola1'}; |
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62 my $colb1 = $retVars{'colb1'}; |
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63 my $cola2 = $retVars{'cola2'}; |
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64 my $colb2 = $retVars{'colb2'}; |
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65 my $firstColFile1 = $retVars{'file1FirstColToCopy'}; |
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66 my $lastColFile1 = $retVars{'file1LastColToCopy'}; |
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67 my $firstColFile2 = $retVars{'file2FirstColToCopy'}; |
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68 my $lastColFile2 = $retVars{'file2LastColToCopy'}; |
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69 my %genes2 = (); |
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70 my %genes4 = (); |
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71 my %genes4key = (); |
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72 my $lineCtr = 0; |
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73 my @cols = (); |
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74 my $firstLineFile2 = $FHFile2->getline(); |
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75 $firstLineFile2 =~ s/\s+$//; |
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76 @cols = split "\t",$firstLineFile2; |
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77 my $numColFile2 = @cols; |
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78 if($firstColFile2==-1){ |
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79 $firstColFile2 = 0; |
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80 $lastColFile2 = $numColFile2-1; |
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81 } |
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82 my @titleFile2 = @cols[$firstColFile2..$lastColFile2]; |
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83 while (my $line = $FHFile2->getline()) { |
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84 $lineCtr++; |
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85 #$line =~ s/\s+$//; |
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86 $line =~ s/\R//g; ##CMS 11-6-14 |
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87 chomp($line); |
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88 @cols = split "\t",$line; |
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89 my $numCols = (@cols + 0); |
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90 |
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91 #$cols[$cola2] = uc($cols[$cola2]); ##CMS 11-6-14 |
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92 #$cols[$colb2] = uc($cols[$colb2]); ##CMS 11-6-14 |
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93 $cols[$cola2] =~ s/ //g; |
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94 my $colsBSymbol = ""; |
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95 if ($cols[$colb2] =~ /\"{0,1}CDS\; ([^\;]+);/) { |
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96 $colsBSymbol = $1; |
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97 } |
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98 else { |
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99 #if ($numCols == ($colb2 +1)) { ##CMS COMMENTED OUT 11-6-14 |
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100 #print "$line\n"; |
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101 #print "Please check this line\n"; |
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102 #exit; |
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103 #} ##CMS END COMMENTS 11-6-14 |
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104 $cols[$colb2] =~ s/ //g; |
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105 $colsBSymbol = $cols[$colb2]; |
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106 } |
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107 if($numCols<$lastColFile2){ |
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108 for(my $i = $numCols;$i<$lastColFile2;$i++){ |
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109 $cols[$i] = ""; |
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110 } |
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111 } |
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112 |
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113 $genes2{$cols[$cola2]} = join("\t",@cols[$firstColFile2..$lastColFile2]); |
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114 $genes4{$colsBSymbol}->{$cols[$cola2]} = join("\t",@cols[$firstColFile2..$lastColFile2]); |
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115 $genes4key{$colsBSymbol}="x"; |
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116 } |
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117 print "linectr: $lineCtr\n"; |
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118 $lineCtr = 0; |
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119 @cols = (); |
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120 my $firstLineFile1 = $FHFile1->getline(); |
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121 $firstLineFile1 =~ s/\s+$//; |
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122 @cols = split "\t",$firstLineFile1; |
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123 my $numColFile1 = @cols; |
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124 if($firstColFile1==-1){ |
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125 $firstColFile1 = 0; |
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126 $lastColFile1 = $numColFile1-1; |
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127 } |
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128 #print "numcolsfile1: $numColFile1\n"; |
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129 #print "lastcolsfile1: $lastColFile1\n"; |
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130 |
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131 my @titleFile1 = @cols[$firstColFile1..$lastColFile1]; |
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132 #print "tf1: @titleFile1\n"; |
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133 #print "tf2: @titleFile2\n"; |
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134 #print "outfile: $OutFile\n"; |
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135 |
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136 print $OutFile join("\t",@titleFile1)."\t".join("\t",@titleFile2)."\n"; |
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137 #my $numCol = $lastColFile1 - $firstColFile1 +1; |
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138 my $numCurrentLine =0; |
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139 while (my $line = $FHFile1->getline()) { |
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140 $lineCtr++; |
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141 $line =~ s/\s+$//; |
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142 my $selectedEntries; |
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143 @cols = split "\t",$line; |
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144 $numCurrentLine = $#cols;#[$firstColFile1..$LastColFile1]; |
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145 #print "numcurrentline: $numCurrentLine\n"; |
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146 $line = $line."\t"; |
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147 if($numCurrentLine<$lastColFile1){ |
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148 #print "in if\n"; |
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149 for(my $i =$numCurrentLine+1;$i<=$lastColFile1;$i++){ |
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150 #print "in for. i=$i\n"; |
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151 $cols[$i]=""; |
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152 #$line = $line."\t"; |
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153 } |
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154 } |
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155 $selectedEntries = join("\t",@cols[$firstColFile1..$lastColFile1]); |
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156 my $numCols = (@cols + 0); |
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157 #$cols[$cola1] = uc($cols[$cola1]); ##CMS 11-6-14 |
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158 #$cols[$colb1] = uc($cols[$colb1]); ##CMS 11-6-14 |
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159 $cols[$cola1] =~ s/ //g; |
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160 my $colsBSymbol = ""; |
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161 if ($cols[$colb1] =~ /\"{0,1}CDS\; ([^\;]+);/) { |
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162 $colsBSymbol = $1; |
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163 } |
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164 else { |
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165 #if ($numCols == ($colb1 +1)) { ##CMS COMMENTED 11-6-14 |
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166 # print"$line"; |
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167 # print " please check this line\n"; |
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168 # exit; |
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169 #} ##CMS END COMMENTS 11-6-14 |
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170 $cols[$colb1] =~ s/ //g; |
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171 $colsBSymbol = $cols[$colb1]; |
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172 } |
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173 if((exists ($genes2{$cols[$cola1]}) and $cols[$cola1] ne "N/A") or (exists ($genes2{$colsBSymbol}) and $colsBSymbol ne "N/A") ) { |
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174 if (exists ($genes2{$cols[$cola1]})) { |
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175 print $OutFile "$selectedEntries"."\t".$genes2{$cols[$cola1]}."\n"; |
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176 } |
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177 elsif (exists ($genes2{$colsBSymbol})) { |
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178 print $OutFile "$selectedEntries"."\t".$genes2{$colsBSymbol}."\n"; |
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179 } |
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180 else { |
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181 print "WHOA, we've got a problem Here!!!!!\n"; |
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182 } |
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183 } |
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184 elsif(exists ($genes4key{$colsBSymbol}) and $colsBSymbol ne "N/A" ) { |
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185 foreach my $symbol (keys %{$genes4{$colsBSymbol}}){ |
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186 print $OutFile "$selectedEntries"."\t".$genes4{$colsBSymbol}->{$symbol}."\n"; |
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187 } |
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188 } |
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189 else { |
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190 print $OutFile "$selectedEntries"."\n"; |
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191 } |
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192 } |
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193 exit; |