1 #!/usr/bin/perl -w 2 # 3 # File: ElementalAnalysis.pl 4 # Author: Manish Sud <msud@san.rr.com> 5 # 6 # Copyright (C) 2024 Manish Sud. All rights reserved. 7 # 8 # This file is part of MayaChemTools. 9 # 10 # MayaChemTools is free software; you can redistribute it and/or modify it under 11 # the terms of the GNU Lesser General Public License as published by the Free 12 # Software Foundation; either version 3 of the License, or (at your option) any 13 # later version. 14 # 15 # MayaChemTools is distributed in the hope that it will be useful, but without 16 # any warranty; without even the implied warranty of merchantability of fitness 17 # for a particular purpose. See the GNU Lesser General Public License for more 18 # details. 19 # 20 # You should have received a copy of the GNU Lesser General Public License 21 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or 22 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, 23 # Boston, MA, 02111-1307, USA. 24 # 25 26 use strict; 27 use FindBin; use lib "$FindBin::Bin/../lib"; 28 use Getopt::Long; 29 use File::Basename; 30 use Text::ParseWords; 31 use Benchmark; 32 use FileUtil; 33 use TextUtil; 34 use MolecularFormula; 35 36 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 37 38 # Autoflush STDOUT 39 $| = 1; 40 41 # Starting message... 42 $ScriptName = basename($0); 43 print "\n$ScriptName: Starting...\n\n"; 44 $StartTime = new Benchmark; 45 46 # Get the options and setup script... 47 SetupScriptUsage(); 48 if ($Options{help}) { 49 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 50 } 51 52 print "Processing options...\n"; 53 my(%OptionsInfo); 54 ProcessOptions(); 55 56 PerformElementalAnalysis(); 57 58 print "\n$ScriptName:Done...\n\n"; 59 60 $EndTime = new Benchmark; 61 $TotalTime = timediff ($EndTime, $StartTime); 62 print "Total time: ", timestr($TotalTime), "\n"; 63 64 ############################################################################### 65 66 # Elemental analysis... 67 sub PerformElementalAnalysis { 68 my($Formula, $FormulaDataRef, $ValueLabel, $CalculationType, $CalculatedValue, $ElementsRef, $ElementCompositionRef, $Status, $ErrorMsg, @ValueLabels, @CalculatedValues); 69 70 print "Performing elemental analysis...\n"; 71 72 if ($OptionsInfo{FileOutput}) { 73 print "Generating file $OptionsInfo{OutFileName}...\n"; 74 open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n"; 75 } 76 77 # Setup value labels... 78 @ValueLabels = (); 79 if ($OptionsInfo{RowsOutput}) { 80 push @ValueLabels, "Formula"; 81 } 82 for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) { 83 push @ValueLabels, $OptionsInfo{ValueLabelsMap}{$CalculationType}; 84 } 85 86 if ($OptionsInfo{RowsOutput}) { 87 ListHeaderRowData(\@ValueLabels); 88 } 89 90 # Go over specified properties... 91 FORMULA: for $Formula (@{$OptionsInfo{SpecifiedFormulas}}) { 92 if (!$OptionsInfo{RowsOutput}) { 93 if ($OptionsInfo{FileOutput}) { 94 print OUTFILE "\nPerforming elemental analysis using formula $Formula...\n\n"; 95 } 96 else { 97 print "\nPerforming elemental analysis using formula $Formula...\n\n"; 98 } 99 } 100 # Calculate appropriate values and write 'em out... 101 if ($OptionsInfo{CheckFormula}) { 102 ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($Formula); 103 if (!$Status) { 104 warn("Warning: Ignoring formula $Formula: It's not a valid value: $ErrorMsg\n"); 105 next FORMULA; 106 } 107 } 108 @CalculatedValues = (); 109 if ($OptionsInfo{RowsOutput}) { 110 push @CalculatedValues, $Formula; 111 } 112 for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) { 113 if ($CalculationType =~ /^ElementalAnalysis$/i) { 114 ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($Formula); 115 $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : ''; 116 } 117 elsif ($CalculationType =~ /^MolecularWeight$/i) { 118 $CalculatedValue = MolecularFormula::CalculateMolecularWeight($Formula); 119 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : ""; 120 } 121 elsif ($CalculationType =~ /^ExactMass$/i) { 122 $CalculatedValue = MolecularFormula::CalculateExactMass($Formula); 123 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : ""; 124 } 125 else { 126 $CalculatedValue = ''; 127 } 128 push @CalculatedValues, $CalculatedValue; 129 } 130 # List data... 131 ListFormulaData(\@ValueLabels, \@CalculatedValues); 132 } 133 if ($OptionsInfo{FileOutput}) { 134 close OUTFILE; 135 } 136 print "\n"; 137 } 138 139 # List calculated data values... 140 sub ListFormulaData { 141 my($DataLabelRef, $DataValueRef) = @_; 142 my($Index, $Line, $Value); 143 144 if ($OptionsInfo{RowsOutput}) { 145 $Line = ''; 146 # Format data... 147 if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) { 148 $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 149 } 150 else { 151 # Always quote values containing commas... 152 $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0]; 153 for $Index (1 .. $#{$DataValueRef} ) { 154 $Value = $DataValueRef->[$Index]; 155 if ($Value =~ /\,/) { 156 $Value = qq("$Value"); 157 } 158 $Line .= $OptionsInfo{OutDelim} . $Value; 159 } 160 } 161 if ($OptionsInfo{FileOutput}) { 162 print OUTFILE "$Line\n"; 163 } 164 else { 165 print "$Line\n"; 166 } 167 } 168 else { 169 # Format and list data... 170 $Line = ''; 171 for $Index (0 .. $#{$DataLabelRef} ) { 172 $Line = $DataLabelRef->[$Index] . ': ' . $DataValueRef->[$Index]; 173 if ($OptionsInfo{FileOutput}) { 174 print OUTFILE "$Line\n"; 175 } 176 else { 177 print "$Line\n"; 178 } 179 } 180 } 181 } 182 183 # List calculated data for a formula... 184 sub ListHeaderRowData { 185 my($DataLabelRef) = @_; 186 my($Line); 187 188 # Format data... 189 $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 190 $Line =~ s/\://g; 191 # List data... 192 if ($OptionsInfo{FileOutput}) { 193 print OUTFILE "$Line\n"; 194 } 195 else { 196 print "$Line\n"; 197 } 198 } 199 200 # Process option values... 201 sub ProcessOptions { 202 %OptionsInfo = (); 203 204 $OptionsInfo{Mode} = $Options{mode}; 205 206 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,"); 207 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0; 208 209 $OptionsInfo{Output} = $Options{output}; 210 $OptionsInfo{OutputStyle} = $Options{outputstyle}; 211 212 $OptionsInfo{RowsOutput} = ($Options{outputstyle} =~ /^FormulaRows$/i) ? 1 : 0; 213 $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0; 214 $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1; 215 216 $OptionsInfo{Precision} = $Options{precision}; 217 218 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef; 219 $OptionsInfo{ValueLabels} = defined $Options{valuelabels} ? $Options{valuelabels} : undef; 220 221 # Setup formulas... 222 @{$OptionsInfo{SpecifiedFormulas}} = (); 223 if (@ARGV >= 1) { 224 push @{$OptionsInfo{SpecifiedFormulas}}, @ARGV; 225 } 226 else { 227 # Setup mode specified default values... 228 push @{$OptionsInfo{SpecifiedFormulas}}, 'H2O'; 229 } 230 231 # Setup what to calculate... 232 @{$OptionsInfo{SpecifiedCalculations}} = (); 233 if ($Options{mode} =~ /^All$/i) { 234 @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass); 235 } 236 else { 237 my($Mode, $ModeValue, @SpecifiedModeValues); 238 $Mode = $Options{mode}; 239 $Mode =~ s/ //g; 240 @SpecifiedModeValues = split /\,/, $Mode; 241 for $ModeValue (@SpecifiedModeValues) { 242 if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) { 243 if ($ModeValue =~ /^All$/i) { 244 die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n"; 245 } 246 else { 247 die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"; 248 } 249 } 250 push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue; 251 } 252 } 253 my($Index, $Value, $Label); 254 # Set up labels for calculated values... 255 @{$OptionsInfo{SpecifiedValueLabels}} = (); 256 if ($Options{valuelabels}) { 257 my($Value, $Label, @ValueLabels); 258 @ValueLabels = split /\,/, $Options{valuelabels}; 259 if (@ValueLabels % 2) { 260 die "Error: The value specified, $Options{valuelabels}, for option \"-v --valuelabels\" is not valid: It must contain even number of comma delimited values\n"; 261 } 262 for ($Index = 0; $Index < @ValueLabels; $Index +=2) { 263 $Value = $ValueLabels[$Index]; 264 $Value =~ s/ //g; 265 $Label = $ValueLabels[$Index + 1]; 266 if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) { 267 die "Error: The value specified, $Value, using option \"-v --valuelabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"; 268 } 269 push @{$OptionsInfo{SpecifiedValueLabels}}, ($Value, $Label); 270 } 271 } 272 273 # Set up calculation type to label map... 274 %{$OptionsInfo{ValueLabelsMap}} = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass'); 275 if (@{$OptionsInfo{SpecifiedValueLabels}}) { 276 for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueLabels}}; $Index +=2) { 277 $Value = $OptionsInfo{SpecifiedValueLabels}[$Index]; 278 $Label = $OptionsInfo{SpecifiedValueLabels}[$Index + 1]; 279 if (exists $OptionsInfo{ValueLabelsMap}{$Value}) { 280 $OptionsInfo{ValueLabelsMap}{$Value} = $Label; 281 } 282 } 283 } 284 285 # Setup output file name... 286 $OptionsInfo{OutFileName} = ''; 287 if ($OptionsInfo{FileOutput}) { 288 my($OutFileRoot, $OutFileExt); 289 290 $OutFileRoot = ''; 291 $OutFileExt = "csv"; 292 if ($Options{outdelim} =~ /^tab$/i) { 293 $OutFileExt = "tsv"; 294 } 295 if ($Options{root}) { 296 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root}); 297 if ($RootFileName && $RootFileExt) { 298 $OutFileRoot = $RootFileName; 299 } 300 else { 301 $OutFileRoot = $Options{root}; 302 } 303 } 304 else { 305 $OutFileRoot = 'FormulasElementalAnalysis'; 306 } 307 $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt; 308 if (!$Options{overwrite}) { 309 if (-e $OptionsInfo{OutFileName}) { 310 die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"; 311 } 312 } 313 } 314 } 315 316 317 # Setup script usage and retrieve command line arguments specified using various options... 318 sub SetupScriptUsage { 319 320 # Retrieve all the options... 321 %Options = (); 322 $Options{mode} = "All"; 323 $Options{outdelim} = "comma"; 324 $Options{output} = "STDOUT"; 325 $Options{outputstyle} = "FormulaBlock"; 326 $Options{precision} = 2; 327 $Options{quote} = "yes"; 328 329 if (!GetOptions(\%Options, "help|h", "fast", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "quote|q=s", "root|r=s", "valuelabels|v=s", "workingdir|w=s")) { 330 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 331 } 332 if ($Options{workingdir}) { 333 if (! -d $Options{workingdir}) { 334 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 335 } 336 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 337 } 338 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 339 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 340 } 341 if ($Options{output} !~ /^(STDOUT|File)$/i) { 342 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"; 343 } 344 if ($Options{outputstyle} !~ /^(FormulaBlock|FormulaRows)$/i) { 345 die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: FormulaBlock or FormulaRows\n"; 346 } 347 if (!IsPositiveInteger($Options{precision})) { 348 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"; 349 } 350 if ($Options{quote} !~ /^(yes|no)$/i) { 351 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 352 } 353 } 354