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planemo upload commit b9501ecca66b6a66c8cb87b945ad5f95181d7790-dirty
author marpiech
date Thu, 06 Oct 2016 07:09:26 -0400
parents 75f2b4087722
children
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1 #!/usr/bin/perl
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2 # Produces text summaries of SD records *
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3 # *
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4 # Usage: sdreport [-l] [-t] [-s<DataField>] [sdFiles] *
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5 # *
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6 # -l output data fields for each record as processed *
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7 # -t tabulate Rbt.Score.* fields for each record as processed *
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8 # -s summarise data fields for all records *
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9 # -s<DataField> summarise data fields for each unique value *
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10 # of <DataField> *
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11 # *
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12 # Note: If -l or -t are combined with -s, the listing/table is output *
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13 # within each ligand summary *
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14 # If sdFiles not given, reads from standard input *
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15 # Output is to standard output *
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16 # Default is equivalent to sdfilter -l *
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17 #*******************************************************************************
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18 use lib "$ENV{'RBT_ROOT'}/lib";
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19
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20 use SDRecord;
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21
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22 # Default field names and headings for rDock v4.00 scores
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23 my @defaultFields = ('SCORE','SCORE.INTER','SCORE.INTRA','SCORE.RESTR','SCORE.INTER.VDW');
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24 my @defaultHeadings = ('TOTAL','INTER','INTRA','RESTR','VDW');
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25
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26 # Default field names and headings for normalised scores (score / #ligand heavy atoms)
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27 my @defaultNormFields = ('SCORE.norm','SCORE.INTER.norm','SCORE.INTRA.norm','SCORE.RESTR.norm','SCORE.heavy');
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28 my @defaultNormHeadings = ('TOTALn','INTERn','INTRAn','RESTRn','#heavy');
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29
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30 # Default field names and headings for rDock v3.00 scores
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31 my @defaultOldFields = ('Rbt.Score.Corrected','Rbt.Score.Inter','Rbt.Score.Intra','Rbt.Score.IntraMin','Rbt.Score.Restraint');
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32 my @defaultOldHeadings = ('TOTAL','INTER','INTRA','INTRAMIN','RESTR');
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33
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34 my $listFormat = 0;
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35 my $summaryFormat = 0;
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36 my $tableFormat = 0;
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37 my $supplierFormat = 0;
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38 my $csvFormat = 0;
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39 my $summaryKey = "_TITLE1";
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40 my $oldFields = 0;#If true, use old default field names for component scores
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41 my $headings = 1;#DM 21 Nov 2000, If false, don't output headings
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42 my @outputFields;
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43 my @outputHeadings;
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44
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45 #Print help if no command line arguments
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46 printHelpAndExit() if (scalar(@ARGV) == 0);
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47
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48 #Parse command line arguments
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49 my $nArgs = scalar(@ARGV);
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50
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51 while (scalar(@ARGV)) {
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52 my $arg = shift @ARGV;
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53 printHelpAndExit() if ($arg eq '-h');
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54 if (index($arg,'-l')==0) {
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55 $listFormat = 1;
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56 }
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57 elsif (index($arg,'-o')==0) {
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58 $oldFields = 1;
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59 }
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60 # 7 Feb 2005 (DM) Option to report normalised aggregate scores
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61 elsif (index($arg,'-norm')==0) {
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62 $oldFields = 2;
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63 }
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64 elsif (index($arg,'-sup')==0) {
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65 $supplierFormat = 1;
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66 }
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67 elsif (index($arg,'-s')==0) {
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68 $summaryFormat = 1;
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69 }
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70 elsif (index($arg,'-id')==0) {
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71 $summaryKey = substr($arg,3);
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72 }
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73 elsif (index($arg,'-nh')==0) {
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74 $headings = 0;
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75 }
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76 elsif (index($arg,'-t')==0) {
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77 $tableFormat = 1;
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78 push @outputFields, split(',',substr($arg,2));
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79 push @outputHeadings, @outputFields;
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80 }
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81 elsif (index($arg,'-c')==0) {
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82 $csvFormat = 1;
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83 push @outputFields, split(',',substr($arg,2));
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84 push @outputHeadings, @outputFields;
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85 }
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86 else {
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87 push @files,$arg;#must be a filename
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88 }
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89 }
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90 push @ARGV,@files;#put the filenames back in the arg list
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91
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92 #use -l if neither table format is specified
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93 $listFormat = (!$tableFormat && !$csvFormat && !$supplierFormat);
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94
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95 #If no output fields defined for -t or -c use the defaults (old or new)
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96 if (scalar(@outputFields)==0) {
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97 if ($oldFields == 1) {
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98 @outputFields = @defaultOldFields;
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99 @outputHeadings = @defaultOldHeadings;
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100 }
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101 elsif ($oldFields == 2) {
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102 @outputFields = @defaultNormFields;
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103 @outputHeadings = @defaultNormHeadings;
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104 }
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105 else {
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106 @outputFields = @defaultFields;
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107 @outputHeadings = @defaultHeadings;
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108 }
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109 }
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110
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111 my $sdRec = new SDRecord;
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112 my %summary;#hash of SDRecord lists, indexed by user-defined summary key
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113 my %indexByName;
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114 my %indexByNum;
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115 my $idx = 0;
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116 my $nRec = 0;
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117
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118 #Column headings for tab and csv format
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119 #DM 21 Nov 2000 - if $headings is false, then don't output the column headings
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120 if ($tableFormat && !$summaryFormat && $headings) {
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121 tabHeadings($summaryKey,@outputHeadings);
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122 }
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123 if ($csvFormat && !$summaryFormat && $headings) {
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124 csvHeadings($summaryKey,@outputHeadings);
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125 }
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126
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127 #read records
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128 while ($sdRec->readRec('LINES'=>1,'DATA'=>1)) {
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129 $sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
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130 if ($listFormat && !$summaryFormat) {
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131 print "\n\nRECORD #$nRec\n";
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132 $sdRec->writeData();
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133 }
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134 if ($tableFormat && !$summaryFormat) {
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135 @recList = ($sdRec);
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136 tabScores(\@recList,$summaryKey,@outputFields);
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137 }
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138 elsif ($csvFormat && !$summaryFormat) {
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139 @recList = ($sdRec);
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140 csvScores(\@recList,$summaryKey,@outputFields);
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141 }
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142 elsif ($supplierFormat && !$summaryFormat) {
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143 @recList = ($sdRec);
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144 tabulateSuppliers(\@recList,$summaryKey);
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145 }
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146 #add record to summary, indexed by user field value
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147 #keep a separate index of unique values of user field values,
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148 #indexed by number in the order the values first appear
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149 #In this way we can maintain the sorted order of ligands
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150 #when we come to print out the summary
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151 if ($summaryFormat) {
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152 my $summaryValue = $sdRec->{'DATA'}->{$summaryKey};
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153 #New data field value encountered
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154 if (!defined $indexByName{$summaryValue}) {
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155 $idx++;#incr the number of unique values
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156 #keep cross-referenced indexes (field value <-> number)
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157 $indexByName{$summaryValue} = $idx;
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158 $indexByNum{$idx} = $summaryValue;
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159 }
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160 push @{$summary{$summaryValue}},$sdRec->copy('DATA'=>1);
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161 }
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162 }
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163
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164 #Print summary if required
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165 if ($summaryFormat) {
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166 print "\n===============================================================\n";
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167 print "SUMMARY BY $summaryKey\n";
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168 foreach $idx (sort {$a<=>$b} keys %indexByNum) {#numberic sort of index numbers
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169 my $key = $indexByNum{$idx};#look up corresponding data field value
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170 print "\n===============================================================\n";
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171 print "$summaryKey = $key (#$idx)\n\n";
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172 writeSummary($summary{$key});
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173 if ($listFormat) {
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174 print "\nIndividual records:\n";
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175 foreach $rec (@{$summary{$key}}) {
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176 print "\n";
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177 $rec->writeData();
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178 }
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179 }
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180 if ($tableFormat) {
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181 print "\nScores:\n";
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182 tabHeadings($summaryKey,@outputHeadings);
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183 tabScores($summary{$key},$summaryKey,@outputFields);
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184 }
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185 if ($csvFormat) {
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186 print "\nScores:\n";
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187 csvHeadings($summaryKey,@outputHeadings);
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188 csvScores($summary{$key},$summaryKey,@outputFields);
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189 }
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190 }
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191 }
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192
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193 ##############################################################
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194 # writes a summary to STDOUT for a list of SDRecords
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195 # Input is a reference to an array of SDRecords
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196 sub writeSummary {
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197 my $recListRef = shift;
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198
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199 #Extract the list of data values for each fieldname into a hash array
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200 #(key=fieldname, value=array ref)
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201 my %fields;
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202 foreach $rec (@{$recListRef}) {
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203 my ($key,$value);
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204 while ( ($key,$value) = each %{$rec->{'DATA'}}) {
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205 push @{$fields{$key}},$value;
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206 }
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207 }
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208
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209 #Look for constant fields and store separately
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210 my %constFields;
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211 foreach $key (keys %fields) {
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212 my @values = sort @{$fields{$key}};
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213 my $nVal = scalar(@values);
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214 if ($values[0] eq $values[$nVal -1]) {
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215 $constFields{$key} = $values[0];#store the field name and the constant value
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216 delete $fields{$key};#remove from (non-const) array
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217 }
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218 }
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219
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220 #Print constant fields
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221 print "\nConstant fields:\n\n";
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222 foreach $key (sort keys %constFields) {
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223 printf "%-40s%s\n",$key,$constFields{$key};
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224 }
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225 #Print min and max value for non-const fields
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226 print "\nVariable fields:\n\n";
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227 foreach $key (sort keys %fields) {
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228 my @values = @{$fields{$key}};
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229 #Look at first value to decide whether to do text or numeric sort
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230 if (isNaN($values[0])) {
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231 @values = sort @values;#text sort
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232 }
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233 else {
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234 @values = sort {$a <=> $b} @values;#numeric sort
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235 }
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236 my $nVal = scalar(@values);
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237 printf "%-40s",$key;
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238 print "Min = $values[0]\tMax = $values[$nVal-1]\t(N = $nVal)\n";
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239 }
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240 }
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241
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242 ##############################################################
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243 # function isNaN equivalent to the C++, java, javascript isNaN
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244 # From P Vaglio, ~intranet/lib/rbt_func.pl
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245 sub isNaN {
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246 local($_) = @_;
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247 s/\s+//g; # strip white space
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248 # match +or- beginning of line 0 or 1 time
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249 # then any numeric 0 or more
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250 # then a decimal point
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251 # then any numeric 0 or more after decimal point
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252 # then possibly an e or E then + or - then any numreci at least once
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253 if (/^([+-]?)(\d*)(\.(\d*))?([Ee]([+-]?\d+))?$/ && (defined $2 || defined $4)) {
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254 return 0;
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255 } else {
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256 return 1;
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257 }
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258 }
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259
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260 ##############################################################
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261 # output corresponding headings for use with tabScores
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262 sub tabHeadings {
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263 my $summaryKey = shift;
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264 my @fieldNames = @_;
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265 printf("%-10s%-30s","REC",$summaryKey);
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266 foreach $field (@fieldNames) {
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267 printf("%10s",$field);
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268 }
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269 print "\n";
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270 }
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271
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272 ##############################################################
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273 # tab-delimited output of named data field values
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274 sub tabScores {
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275 my $recListRef = shift;
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276 my $summaryKey = shift;
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277 my @fieldNames = @_;
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278 foreach $rec (@{$recListRef}) {
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279 printf("%03d\t%-30.30s",$rec->{'DATA'}->{'_REC'},$rec->{'DATA'}->{$summaryKey});
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280 foreach $field (@fieldNames) {
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281 my $val = $rec->{'DATA'}->{$field};
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282 if (isNaN($val)) {
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283 printf("%-10.12s",$val);
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284 }
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285 else {
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286 printf("%10.3f",$val);
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287 }
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288 }
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289 print "\n";
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290 }
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291 }
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292
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293 ##############################################################
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294 # output corresponding headings for use with csvScores
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295 sub csvHeadings {
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296 my $summaryKey = shift;
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297 my @fieldNames = @_;
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298 printf("%s,%s","REC",$summaryKey);
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299 foreach $field (@fieldNames) {
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300 printf(",%s",$field);
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301 }
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302 print "\n";
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303 }
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304
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305 ##############################################################
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306 # comma-delimited output of named data field values
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307 sub csvScores {
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308 my $recListRef = shift;
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309 my $summaryKey = shift;
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310 my @fieldNames = @_;
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311 foreach $rec (@{$recListRef}) {
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312 printf("%d,%s",$rec->{'DATA'}->{'_REC'},$rec->{'DATA'}->{$summaryKey});
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313 foreach $field (@fieldNames) {
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314 my $val = $rec->{'DATA'}->{$field};
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315 if (isNaN($val)) {
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316 printf(",%s",$val);
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317 }
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318 else {
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319 printf(",%.3f",$val);
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320 }
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321 }
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322 print "\n";
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323 }
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324 }
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325
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326
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327 ##############################################################
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328 # standardised output of Catalyst supplier field
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329 # Input is a reference to an array of SDRecords
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330 # and a ligand identifier field to output in column 1 (def=Name)
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331 sub tabulateSuppliers {
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332 my $recListRef = shift;
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333 my $summaryKey = shift || 'Name';
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334 foreach $rec (@{$recListRef}) {
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335 my $suppBase = $rec->{'DATAREF'}->{'Supplier'}+1;
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336 my $linesRef = $rec->{'LINES'};
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337 my $name = $rec->{'DATA'}->{$summaryKey};
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338
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339 #Output some useful compound info
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340 my $name = $rec->{'DATA'}->{$summaryKey};
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341 my $molFormula = $rec->{'DATA'}->{'MolFormula'};
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342 my $molWt = $rec->{'DATA'}->{'MolWt'};
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343 my $casNum = $rec->{'DATA'}->{'CAS_num'};
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344 my $mdlNum = $rec->{'DATA'}->{'MDLNUMBER'};
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345 print "\n\n====================================================================================================\n";
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346 printf("%-10.10s%s\n","Name:",$name);
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347 printf("%-10.10s%s\n","Formula:",$molFormula);
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348 printf("%-10.10s%s\n","Mol.wt:",$molWt);
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349 printf("%-10.10s%s\n","CAS #:",$casNum);
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350 printf("%-10.10s%s\n","MDL #:",$mdlNum);
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351
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352 #Get all the supplier record lines into a list
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353 #Record is terminated by blank line
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354 my @lines;
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355 my $nLines = 0;
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356 for (; $$linesRef[$suppBase+$nLines] ne ""; $nLines++) {
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357 push @lines,$$linesRef[$suppBase+$nLines];
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358 }
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359
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360 #Column headings
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361 printf("\n%-20.20s%-40.40s%-40.40s\n",
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362 "Supplier",
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363 "Comment",
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364 "Price"
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365 );
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366 print "----------------------------------------------------------------------------------------------------\n";
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367
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368 #Loop over each supplier
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369 my $iLine = 0;
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370 for (; $iLine < $nLines; $iLine++) {
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371 #collect supplier info lines
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372 my @supplierInfo = ();
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373 for (; $lines[$iLine] ne "." && $iLine < $nLines; $iLine++) {
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374 push @supplierInfo,$lines[$iLine];
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375 }
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376 #Check for incomplete record
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377 if ($iLine == $nLines) {
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378 print "** INCOMPLETE RECORD **\n";
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379 last;
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380 }
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381 my $nSupplierInfo = scalar(@supplierInfo);
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marpiech
parents:
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382 my $supplier = $supplierInfo[0];
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marpiech
parents:
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383 #loop over each grade
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marpiech
parents:
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384 for ($iLine++; ($lines[$iLine] ne "........................") && ($iLine < $nLines); $iLine++) {
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marpiech
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385 #collect grade info lines
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marpiech
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386 my @gradeInfo = ();
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marpiech
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387 for (; index($lines[$iLine],"_") ne 0 && $iLine < $nLines; $iLine++) {
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marpiech
parents:
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388 push @gradeInfo,$lines[$iLine];
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marpiech
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389 }
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marpiech
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390 #Check for incomplete record
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marpiech
parents:
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391 if ($iLine == $nLines) {
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marpiech
parents:
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392 print "** INCOMPLETE RECORD **\n";
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marpiech
parents:
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393 last;
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marpiech
parents:
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394 }
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marpiech
parents:
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395 my $grade = $gradeInfo[0];
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marpiech
parents:
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396 #loop over each price info line
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marpiech
parents:
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397 for (; index($lines[$iLine],".") ne 0 && $iLine < $nLines; $iLine++) {
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marpiech
parents:
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398 my @priceInfo = split(" ",$lines[$iLine]);
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marpiech
parents:
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399 my $price = join(" ",@priceInfo);
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marpiech
parents:
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400 printf("%-20.20s%-40.39s%-40.40s\n",
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marpiech
parents:
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401 $supplier,
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marpiech
parents:
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402 $grade,
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marpiech
parents:
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403 $price);
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marpiech
parents:
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404 }
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marpiech
parents:
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405 #Check for incomplete record
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marpiech
parents:
diff changeset
406 if ($iLine == $nLines) {
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marpiech
parents:
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407 print "** INCOMPLETE RECORD **\n";
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marpiech
parents:
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408 last;
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marpiech
parents:
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409 }
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marpiech
parents:
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410 last if $lines[$iLine] eq "........................";
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marpiech
parents:
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411 }
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marpiech
parents:
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412 }
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marpiech
parents:
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413 }
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marpiech
parents:
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414 }
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marpiech
parents:
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415
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marpiech
parents:
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416
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marpiech
parents:
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417 #######################################################################
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marpiech
parents:
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418 sub printHelpAndExit {
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marpiech
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419 print "\nProduces text summaries of SD records\n";
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marpiech
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420 print "\nUsage:\tsdreport [-l] [-t[<FieldName,FieldName...>]] [-c<FieldName,FieldName...>] [-id<IDField>] [-nh] [-o] [-s] [-sup] [sdFiles]\n";
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marpiech
parents:
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421 print "\n\t-l (list format) output all data fields for each record as processed\n";
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marpiech
parents:
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422 print "\t-t (tab format) tabulate selected fields for each record as processed\n";
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marpiech
parents:
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423 print "\t-c (csv format) comma delimited output of selected fields for each record as processed\n";
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marpiech
parents:
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424 print "\t-s (summary format) output summary statistics for each unique value of ligand ID\n";
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marpiech
parents:
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425 print "\t-sup (supplier format) tabulate supplier details (from Catalyst)\n";
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marpiech
parents:
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426 print "\t-id<IDField> data field to use as ligand ID\n";
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marpiech
parents:
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427 print "\t-nh don't output column headings in -t and -c formats\n";
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marpiech
parents:
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428 print "\t-o use old (v3.00) score field names as default columns in -t and -c formats, else use v4.00 field names\n";
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marpiech
parents:
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429 print "\t-norm use normalised score field names as default columns in -t and -c formats (normalised = score / #ligand heavy atoms)\n";
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marpiech
parents:
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430 print "\nNote:\tIf -l, -t or -c are combined with -s, the listing/table is output within each ligand summary\n";
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marpiech
parents:
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431 print "\t-sup should not be combined with other options\n";
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marpiech
parents:
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432 print "\tDefault field names for -t and -c are rDock score field names\n";
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marpiech
parents:
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433 print "\tDefault ID field name is Name\n";
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marpiech
parents:
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434 print "\n\tIf sdFiles not given, reads from standard input\n";
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marpiech
parents:
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435 print "\tOutput is to standard output\n\n";
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marpiech
parents:
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436 exit;
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marpiech
parents:
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437 }