1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: ElementalAnalysis.pl,v $ 4 # $Date: 2015/02/28 20:46:19 $ 5 # $Revision: 1.19 $ 6 # 7 # Author: Manish Sud <msud@san.rr.com> 8 # 9 # Copyright (C) 2015 Manish Sud. All rights reserved. 10 # 11 # This file is part of MayaChemTools. 12 # 13 # MayaChemTools is free software; you can redistribute it and/or modify it under 14 # the terms of the GNU Lesser General Public License as published by the Free 15 # Software Foundation; either version 3 of the License, or (at your option) any 16 # later version. 17 # 18 # MayaChemTools is distributed in the hope that it will be useful, but without 19 # any warranty; without even the implied warranty of merchantability of fitness 20 # for a particular purpose. See the GNU Lesser General Public License for more 21 # details. 22 # 23 # You should have received a copy of the GNU Lesser General Public License 24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or 25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, 26 # Boston, MA, 02111-1307, USA. 27 # 28 29 use strict; 30 use FindBin; use lib "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Text::ParseWords; 34 use Benchmark; 35 use FileUtil; 36 use TextUtil; 37 use MolecularFormula; 38 39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 40 41 # Autoflush STDOUT 42 $| = 1; 43 44 # Starting message... 45 $ScriptName = basename($0); 46 print "\n$ScriptName: Starting...\n\n"; 47 $StartTime = new Benchmark; 48 49 # Get the options and setup script... 50 SetupScriptUsage(); 51 if ($Options{help}) { 52 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 53 } 54 55 print "Processing options...\n"; 56 my(%OptionsInfo); 57 ProcessOptions(); 58 59 PerformElementalAnalysis(); 60 61 print "\n$ScriptName:Done...\n\n"; 62 63 $EndTime = new Benchmark; 64 $TotalTime = timediff ($EndTime, $StartTime); 65 print "Total time: ", timestr($TotalTime), "\n"; 66 67 ############################################################################### 68 69 # Elemental analysis... 70 sub PerformElementalAnalysis { 71 my($Formula, $FormulaDataRef, $ValueLabel, $CalculationType, $CalculatedValue, $ElementsRef, $ElementCompositionRef, $Status, $ErrorMsg, @ValueLabels, @CalculatedValues); 72 73 print "Performing elemental analysis...\n"; 74 75 if ($OptionsInfo{FileOutput}) { 76 print "Generating file $OptionsInfo{OutFileName}...\n"; 77 open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n"; 78 } 79 80 # Setup value labels... 81 @ValueLabels = (); 82 if ($OptionsInfo{RowsOutput}) { 83 push @ValueLabels, "Formula"; 84 } 85 for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) { 86 push @ValueLabels, $OptionsInfo{ValueLabelsMap}{$CalculationType}; 87 } 88 89 if ($OptionsInfo{RowsOutput}) { 90 ListHeaderRowData(\@ValueLabels); 91 } 92 93 # Go over specified properties... 94 FORMULA: for $Formula (@{$OptionsInfo{SpecifiedFormulas}}) { 95 if (!$OptionsInfo{RowsOutput}) { 96 if ($OptionsInfo{FileOutput}) { 97 print OUTFILE "\nPerforming elemental analysis using formula $Formula...\n\n"; 98 } 99 else { 100 print "\nPerforming elemental analysis using formula $Formula...\n\n"; 101 } 102 } 103 # Calculate appropriate values and write 'em out... 104 if ($OptionsInfo{CheckFormula}) { 105 ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($Formula); 106 if (!$Status) { 107 warn("Warning: Ignoring formula $Formula: It's not a valid value: $ErrorMsg\n"); 108 next FORMULA; 109 } 110 } 111 @CalculatedValues = (); 112 if ($OptionsInfo{RowsOutput}) { 113 push @CalculatedValues, $Formula; 114 } 115 for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) { 116 if ($CalculationType =~ /^ElementalAnalysis$/i) { 117 ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($Formula); 118 $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : ''; 119 } 120 elsif ($CalculationType =~ /^MolecularWeight$/i) { 121 $CalculatedValue = MolecularFormula::CalculateMolecularWeight($Formula); 122 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : ""; 123 } 124 elsif ($CalculationType =~ /^ExactMass$/i) { 125 $CalculatedValue = MolecularFormula::CalculateExactMass($Formula); 126 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : ""; 127 } 128 else { 129 $CalculatedValue = ''; 130 } 131 push @CalculatedValues, $CalculatedValue; 132 } 133 # List data... 134 ListFormulaData(\@ValueLabels, \@CalculatedValues); 135 } 136 if ($OptionsInfo{FileOutput}) { 137 close OUTFILE; 138 } 139 print "\n"; 140 } 141 142 # List calculated data values... 143 sub ListFormulaData { 144 my($DataLabelRef, $DataValueRef) = @_; 145 my($Index, $Line, $Value); 146 147 if ($OptionsInfo{RowsOutput}) { 148 $Line = ''; 149 # Format data... 150 if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) { 151 $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 152 } 153 else { 154 # Always quote values containing commas... 155 $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0]; 156 for $Index (1 .. $#{$DataValueRef} ) { 157 $Value = $DataValueRef->[$Index]; 158 if ($Value =~ /\,/) { 159 $Value = qq("$Value"); 160 } 161 $Line .= $OptionsInfo{OutDelim} . $Value; 162 } 163 } 164 if ($OptionsInfo{FileOutput}) { 165 print OUTFILE "$Line\n"; 166 } 167 else { 168 print "$Line\n"; 169 } 170 } 171 else { 172 # Format and list data... 173 $Line = ''; 174 for $Index (0 .. $#{$DataLabelRef} ) { 175 $Line = $DataLabelRef->[$Index] . ': ' . $DataValueRef->[$Index]; 176 if ($OptionsInfo{FileOutput}) { 177 print OUTFILE "$Line\n"; 178 } 179 else { 180 print "$Line\n"; 181 } 182 } 183 } 184 } 185 186 # List calculated data for a formula... 187 sub ListHeaderRowData { 188 my($DataLabelRef) = @_; 189 my($Line); 190 191 # Format data... 192 $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 193 $Line =~ s/\://g; 194 # List data... 195 if ($OptionsInfo{FileOutput}) { 196 print OUTFILE "$Line\n"; 197 } 198 else { 199 print "$Line\n"; 200 } 201 } 202 203 # Process option values... 204 sub ProcessOptions { 205 %OptionsInfo = (); 206 207 $OptionsInfo{Mode} = $Options{mode}; 208 209 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,"); 210 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0; 211 212 $OptionsInfo{Output} = $Options{output}; 213 $OptionsInfo{OutputStyle} = $Options{outputstyle}; 214 215 $OptionsInfo{RowsOutput} = ($Options{outputstyle} =~ /^FormulaRows$/i) ? 1 : 0; 216 $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0; 217 $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1; 218 219 $OptionsInfo{Precision} = $Options{precision}; 220 221 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef; 222 $OptionsInfo{ValueLabels} = defined $Options{valuelabels} ? $Options{valuelabels} : undef; 223 224 # Setup formulas... 225 @{$OptionsInfo{SpecifiedFormulas}} = (); 226 if (@ARGV >= 1) { 227 push @{$OptionsInfo{SpecifiedFormulas}}, @ARGV; 228 } 229 else { 230 # Setup mode specified default values... 231 push @{$OptionsInfo{SpecifiedFormulas}}, 'H2O'; 232 } 233 234 # Setup what to calculate... 235 @{$OptionsInfo{SpecifiedCalculations}} = (); 236 if ($Options{mode} =~ /^All$/i) { 237 @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass); 238 } 239 else { 240 my($Mode, $ModeValue, @SpecifiedModeValues); 241 $Mode = $Options{mode}; 242 $Mode =~ s/ //g; 243 @SpecifiedModeValues = split /\,/, $Mode; 244 for $ModeValue (@SpecifiedModeValues) { 245 if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) { 246 if ($ModeValue =~ /^All$/i) { 247 die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n"; 248 } 249 else { 250 die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"; 251 } 252 } 253 push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue; 254 } 255 } 256 my($Index, $Value, $Label); 257 # Set up labels for calculated values... 258 @{$OptionsInfo{SpecifiedValueLabels}} = (); 259 if ($Options{valuelabels}) { 260 my($Value, $Label, @ValueLabels); 261 @ValueLabels = split /\,/, $Options{valuelabels}; 262 if (@ValueLabels % 2) { 263 die "Error: The value specified, $Options{valuelabels}, for option \"-v --valuelabels\" is not valid: It must contain even number of comma delimited values\n"; 264 } 265 for ($Index = 0; $Index < @ValueLabels; $Index +=2) { 266 $Value = $ValueLabels[$Index]; 267 $Value =~ s/ //g; 268 $Label = $ValueLabels[$Index + 1]; 269 if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) { 270 die "Error: The value specified, $Value, using option \"-v --valuelabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"; 271 } 272 push @{$OptionsInfo{SpecifiedValueLabels}}, ($Value, $Label); 273 } 274 } 275 276 # Set up calculation type to label map... 277 %{$OptionsInfo{ValueLabelsMap}} = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass'); 278 if (@{$OptionsInfo{SpecifiedValueLabels}}) { 279 for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueLabels}}; $Index +=2) { 280 $Value = $OptionsInfo{SpecifiedValueLabels}[$Index]; 281 $Label = $OptionsInfo{SpecifiedValueLabels}[$Index + 1]; 282 if (exists $OptionsInfo{ValueLabelsMap}{$Value}) { 283 $OptionsInfo{ValueLabelsMap}{$Value} = $Label; 284 } 285 } 286 } 287 288 # Setup output file name... 289 $OptionsInfo{OutFileName} = ''; 290 if ($OptionsInfo{FileOutput}) { 291 my($OutFileRoot, $OutFileExt); 292 293 $OutFileRoot = ''; 294 $OutFileExt = "csv"; 295 if ($Options{outdelim} =~ /^tab$/i) { 296 $OutFileExt = "tsv"; 297 } 298 if ($Options{root}) { 299 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root}); 300 if ($RootFileName && $RootFileExt) { 301 $OutFileRoot = $RootFileName; 302 } 303 else { 304 $OutFileRoot = $Options{root}; 305 } 306 } 307 else { 308 $OutFileRoot = 'FormulasElementalAnalysis'; 309 } 310 $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt; 311 if (!$Options{overwrite}) { 312 if (-e $OptionsInfo{OutFileName}) { 313 die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"; 314 } 315 } 316 } 317 } 318 319 320 # Setup script usage and retrieve command line arguments specified using various options... 321 sub SetupScriptUsage { 322 323 # Retrieve all the options... 324 %Options = (); 325 $Options{mode} = "All"; 326 $Options{outdelim} = "comma"; 327 $Options{output} = "STDOUT"; 328 $Options{outputstyle} = "FormulaBlock"; 329 $Options{precision} = 2; 330 $Options{quote} = "yes"; 331 332 if (!GetOptions(\%Options, "help|h", "fast", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "quote|q=s", "root|r=s", "valuelabels|v=s", "workingdir|w=s")) { 333 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 334 } 335 if ($Options{workingdir}) { 336 if (! -d $Options{workingdir}) { 337 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 338 } 339 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 340 } 341 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 342 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 343 } 344 if ($Options{output} !~ /^(STDOUT|File)$/i) { 345 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"; 346 } 347 if ($Options{outputstyle} !~ /^(FormulaBlock|FormulaRows)$/i) { 348 die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: FormulaBlock or FormulaRows\n"; 349 } 350 if (!IsPositiveInteger($Options{precision})) { 351 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"; 352 } 353 if ($Options{quote} !~ /^(yes|no)$/i) { 354 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 355 } 356 } 357