MayaChemTools

   1 #!/usr/bin/perl -w
   2 #
   3 # File: ElementalAnalysis.pl
   4 # Author: Manish Sud <msud@san.rr.com>
   5 #
   6 # Copyright (C) 2019 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