MayaChemTools

   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