1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: InfoAminoAcids.pl,v $ 4 # $Date: 2015/02/28 20:46:20 $ 5 # $Revision: 1.26 $ 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 "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Text::ParseWords; 34 use Benchmark; 35 use FileUtil; 36 use TextUtil; 37 use AminoAcids; 38 39 my($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 ListAminoAcidProperties(); 60 print "\n$ScriptName:Done...\n\n"; 61 62 $EndTime = new Benchmark; 63 $TotalTime = timediff ($EndTime, $StartTime); 64 print "Total time: ", timestr($TotalTime), "\n"; 65 66 ############################################################################### 67 68 # List data for an amino acid... 69 sub ListAminoAcidData { 70 my($DataLabelRef, $DataValueRef) = @_; 71 my($Index, $Line, $Value); 72 73 if ($OptionsInfo{AminoAcidRowsOutput}) { 74 $Line = ''; 75 # Format data... 76 if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) { 77 $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 78 } 79 else { 80 # Always quote values containing commas... 81 $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0]; 82 for $Index (1 .. $#{$DataValueRef} ) { 83 $Value = $DataValueRef->[$Index]; 84 if ($Value =~ /\,/) { 85 $Value = qq("$Value"); 86 } 87 $Line .= $OptionsInfo{OutDelim} . $Value; 88 } 89 } 90 if ($OptionsInfo{FileOutput}) { 91 print OUTFILE "$Line\n"; 92 } 93 else { 94 print "$Line\n"; 95 } 96 } 97 else { 98 # Format and list data... 99 $Line = ''; 100 for $Index (0 .. $#{$DataLabelRef} ) { 101 $Line = $DataLabelRef->[$Index] . ' ' . $DataValueRef->[$Index]; 102 if ($OptionsInfo{FileOutput}) { 103 print OUTFILE "$Line\n"; 104 } 105 else { 106 print "$Line\n"; 107 } 108 } 109 } 110 } 111 112 # List data for an amino acid... 113 sub ListHeaderRowData { 114 my($DataLabelRef) = @_; 115 my($Line); 116 117 # Format data... 118 $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 119 $Line =~ s/\://g; 120 # List data... 121 if ($OptionsInfo{FileOutput}) { 122 print OUTFILE "$Line\n"; 123 } 124 else { 125 print "$Line\n"; 126 } 127 } 128 129 # List properties for amino acids... 130 sub ListAminoAcidProperties { 131 my($AminoAcidID, $AminoAcidDataRef, $PropertyName, $PropertyValue, @PropertyLabels, @PropertyValues); 132 133 print "Listing information for amino acid(s)...\n"; 134 135 if ($OptionsInfo{FileOutput}) { 136 print "Generating file $OptionsInfo{OutFileName}...\n"; 137 open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n"; 138 } 139 140 # Setup property labels... 141 @PropertyLabels = (); 142 for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) { 143 push @PropertyLabels, ("$PropertyName:"); 144 } 145 146 if ($OptionsInfo{AminoAcidRowsOutput}) { 147 ListHeaderRowData(\@PropertyLabels); 148 } 149 150 # Go over specified properties... 151 for $AminoAcidID (@{$OptionsInfo{SpecifiedAminoAcidIDs}}) { 152 $AminoAcidDataRef = AminoAcids::GetAminoAcidPropertiesData($AminoAcidID); 153 154 if (!$OptionsInfo{AminoAcidRowsOutput}) { 155 if ($OptionsInfo{FileOutput}) { 156 print OUTFILE "\nListing properties for amino acid $AminoAcidID...\n\n"; 157 } 158 else { 159 print "\nListing properties for amino acid $AminoAcidID...\n\n"; 160 } 161 } 162 163 # Collect data.. 164 @PropertyValues = (); 165 for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) { 166 $PropertyValue = $AminoAcidDataRef->{$PropertyName}; 167 if (IsFloat($PropertyValue)) { 168 $PropertyValue = sprintf("%.$OptionsInfo{Precision}f", $PropertyValue) + 0; 169 } 170 push @PropertyValues, $PropertyValue; 171 } 172 # List data... 173 ListAminoAcidData(\@PropertyLabels, \@PropertyValues); 174 } 175 if ($OptionsInfo{FileOutput}) { 176 close OUTFILE; 177 } 178 print "\n"; 179 } 180 181 # Get propery names from categories... 182 sub GetPropertyNamesFromCategories { 183 my($CategoryName) = @_; 184 my(@PropertyNames); 185 186 @PropertyNames = (); 187 if ($CategoryName =~ /^Basic$/i) { 188 @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'ChemicalFormula','MolecularWeight', 'LinearStructure', 'LinearStructureAtpH7.4'); 189 } elsif ($CategoryName =~ /^BasicPlus$/i) { 190 @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'AcidicBasic', 'PolarNonpolar', 'Charged', 'Aromatic', 'HydrophobicHydophilic', 'IsoelectricPoint', 'pKCOOH', 'pKNH3+', 'ChemicalFormula', 'MolecularWeight', 'ExactMass', 'ChemicalFormulaMinusH2O', 'MolecularWeightMinusH2O(18.01524)', 'ExactMassMinusH2O(18.01056)','LinearStructure', 'LinearStructureAtpH7.4'); 191 } elsif ($CategoryName =~ /^BasicAndHydrophobicity$/i) { 192 @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'ChemicalFormula', 'MolecularWeight', 'LinearStructure', 'LinearStructureAtpH7.4', 'HydrophobicityEisenbergAndOthers', 'HydrophobicityHoppAndWoods', 'HydrophobicityJanin', 'HydrophobicityKyteAndDoolittle', 'HydrophobicityRoseAndOthers', 'HydrophobicityWolfendenAndOthers'); 193 } elsif ($CategoryName =~ /^BasicAndHydrophobicityPlus$/i) { 194 @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'ChemicalFormula', 'MolecularWeight', 'LinearStructure', 'LinearStructureAtpH7.4', 'HydrophobicityAbrahamAndLeo', 'HydrophobicityBlack', 'HydrophobicityBullAndBreese', 'HydrophobicityChothia', 'HydrophobicityEisenbergAndOthers', 'HydrophobicityFauchereAndOthers', 'HydrophobicityGuy', 'HydrophobicityHPLCAtpH3.4Cowan', 'HydrophobicityHPLCAtpH7.5Cowan', 'HydrophobicityHPLCParkerAndOthers', 'HydrophobicityHPLCWilsonAndOthers', 'HydrophobicityHoppAndWoods', 'HydrophobicityJanin', 'HydrophobicityKyteAndDoolittle', 'HydrophobicityManavalanAndOthers', 'HydrophobicityMiyazawaAndOthers', 'HydrophobicityOMHSweetAndOthers', 'HydrophobicityRaoAndArgos', 'HydrophobicityRfMobility', 'HydrophobicityRoseAndOthers', 'HydrophobicityRoseman', 'HydrophobicityWellingAndOthers', 'HydrophobicityWolfendenAndOthers'); 195 } 196 197 return @PropertyNames; 198 } 199 200 # Process option values... 201 sub ProcessOptions { 202 %OptionsInfo = (); 203 204 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,"); 205 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0; 206 207 $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef; 208 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef; 209 210 $OptionsInfo{OutputStyle} = $Options{outputstyle}; 211 212 $OptionsInfo{AminoAcidRowsOutput} = ($Options{outputstyle} =~ /^AminoAcidRows$/i) ? 1 : 0; 213 $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0; 214 215 $OptionsInfo{Precision} = $Options{precision}; 216 217 my($AminoAcidID, @AminoAcidIDs); 218 219 @{$OptionsInfo{SpecifiedAminoAcidIDs}} = (); 220 221 # Set up Amino Acids IDs except for All mode... 222 @AminoAcidIDs = (); 223 224 if (@ARGV >= 1) { 225 push @AminoAcidIDs, @ARGV; 226 } 227 else { 228 # Setup mode specified default values... 229 push @AminoAcidIDs, 'Ala'; 230 } 231 232 # Generate list of amino acids... 233 if (@ARGV == 1 && $ARGV[0] =~ /^All$/i) { 234 push @{$OptionsInfo{SpecifiedAminoAcidIDs}}, AminoAcids::GetAminoAcids(); 235 } 236 else { 237 ID: for $AminoAcidID (@AminoAcidIDs) { 238 if (AminoAcids::IsAminoAcid($AminoAcidID)) { 239 push @{$OptionsInfo{SpecifiedAminoAcidIDs}}, $AminoAcidID; 240 } 241 else { 242 warn "Ignoring amino acid ID, $AminoAcidID, specified using command line parameter option: Unknown amino acid ID...\n"; 243 next ID; 244 } 245 } 246 } 247 SetupSpecifiedProperties(); 248 249 # Setup output file name... 250 $OptionsInfo{OutFileName} = ''; 251 if ($OptionsInfo{FileOutput}) { 252 my($OutFileRoot, $OutFileExt); 253 254 $OutFileRoot = ''; 255 $OutFileExt = "csv"; 256 if ($Options{outdelim} =~ /^tab$/i) { 257 $OutFileExt = "tsv"; 258 } 259 if ($Options{root}) { 260 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root}); 261 if ($RootFileName && $RootFileExt) { 262 $OutFileRoot = $RootFileName; 263 } 264 else { 265 $OutFileRoot = $Options{root}; 266 } 267 } 268 else { 269 $OutFileRoot = 'AminoAcidsInfo'; 270 } 271 $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt; 272 if (!$Options{overwrite}) { 273 if (-e $OptionsInfo{OutFileName}) { 274 die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"; 275 } 276 } 277 } 278 } 279 280 # Setup properties to list... 281 sub SetupSpecifiedProperties { 282 283 $OptionsInfo{Properties} = defined $Options{properties} ? $Options{properties} : undef; 284 285 $OptionsInfo{PropertiesMode} = $Options{propertiesmode}; 286 $OptionsInfo{PropertiesListing} = $Options{propertieslisting}; 287 288 # Make sure appropriate properties/category names are specified... 289 @{$OptionsInfo{SpecifiedProperies}} = (); 290 if ($Options{properties} && ($Options{propertiesmode} =~ /^All$/i) ) { 291 warn "Warning: Ignoring values specifed by \"-p --properties\" option: Not valid for All value of \"--propertiesmode\" option...\n"; 292 } 293 if ($Options{propertiesmode} =~ /^All$/i) { 294 if ($Options{propertieslisting} =~ /^Alphabetical$/i) { 295 push @{$OptionsInfo{SpecifiedProperies}}, AminoAcids::GetAminoAcidPropertiesNames('Alphabetical'); 296 } 297 else { 298 push @{$OptionsInfo{SpecifiedProperies}}, AminoAcids::GetAminoAcidPropertiesNames(); 299 } 300 } 301 else { 302 if ($Options{properties}) { 303 if ($Options{propertiesmode} =~ /^Categories$/i) { 304 # Check category name... 305 if ($Options{properties} !~ /^(Basic|BasicPlus|BasicAndHydrophobicity|BasicAndHydrophobicityPlus)$/i) { 306 die "Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic, BasicPlus, BasicAndHydrophobicity, and BasicAndHydrophobicityPlus\n"; 307 } 308 # Set propertynames... 309 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories($Options{properties}); 310 } 311 else { 312 # Check property names.. 313 my($Name, $PropertyName, @Names); 314 @Names = split /\,/, $Options{properties}; 315 NAME: for $Name (@Names) { 316 $PropertyName = RemoveLeadingAndTrailingWhiteSpaces($Name); 317 if (AminoAcids::IsAminoAcidProperty($PropertyName)) { 318 push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName; 319 } 320 else { 321 warn "Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n"; 322 } 323 } 324 if ($Options{propertieslisting} =~ /^Alphabetical$/i) { 325 # ThreeLetterCode, OneLetterCode and AminoAcid are always listed first... 326 # NaturalIsotopeData in the end... 327 my($OneLetterCodePresent, $ThreeLetterCodePresent, $AminoAcidPresent, @AlphabeticalProperties, %PropertiesMap); 328 %PropertiesMap = (); 329 @AlphabeticalProperties = (); 330 $OneLetterCodePresent = 0; $ThreeLetterCodePresent = 0; $AminoAcidPresent = 0; 331 NAME: for $Name (@{$OptionsInfo{SpecifiedProperies}}) { 332 if ($Name =~ /^OneLetterCode$/i) { 333 $OneLetterCodePresent = 1; 334 next NAME; 335 } 336 if ($Name =~ /^ThreeLetterCode$/i) { 337 $ThreeLetterCodePresent = 1; 338 next NAME; 339 } 340 if ($Name =~ /^AminoAcid$/i) { 341 $AminoAcidPresent = 1; 342 next NAME; 343 } 344 $PropertiesMap{$Name} = $Name; 345 } 346 # Setup the alphabetical list... 347 if ($ThreeLetterCodePresent) { 348 push @AlphabeticalProperties, 'ThreeLetterCode'; 349 } 350 if ($OneLetterCodePresent) { 351 push @AlphabeticalProperties, 'OneLetterCode'; 352 } 353 if ($AminoAcidPresent) { 354 push @AlphabeticalProperties, 'AminoAcid'; 355 } 356 for $Name (sort keys %PropertiesMap) { 357 push @AlphabeticalProperties, $Name; 358 } 359 @{$OptionsInfo{SpecifiedProperies}} = (); 360 push @{$OptionsInfo{SpecifiedProperies}}, @AlphabeticalProperties; 361 } 362 } 363 } 364 else { 365 # Set default value... 366 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories('Basic'); 367 } 368 } 369 } 370 371 # Setup script usage and retrieve command line arguments specified using various options... 372 sub SetupScriptUsage { 373 374 # Retrieve all the options... 375 %Options = (); 376 $Options{outdelim} = "comma"; 377 $Options{output} = "STDOUT"; 378 $Options{outputstyle} = "AminoAcidBlock"; 379 $Options{precision} = 4; 380 $Options{propertiesmode} = "Categories"; 381 $Options{propertieslisting} = "ByGroup"; 382 $Options{quote} = "yes"; 383 384 if (!GetOptions(\%Options, "help|h", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "properties|p=s", "propertieslisting=s", "propertiesmode=s", "quote|q=s", "root|r=s", "workingdir|w=s")) { 385 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 386 } 387 if ($Options{workingdir}) { 388 if (! -d $Options{workingdir}) { 389 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 390 } 391 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 392 } 393 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 394 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 395 } 396 if ($Options{output} !~ /^(STDOUT|File)$/i) { 397 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"; 398 } 399 if ($Options{outputstyle} !~ /^(AminoAcidBlock|AminoAcidRows)$/i) { 400 die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: AminoAcidBlock or AminoAcidRows\n"; 401 } 402 if (!IsPositiveInteger($Options{precision})) { 403 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"; 404 } 405 if ($Options{propertiesmode} !~ /^(Categories|Names|All)$/i) { 406 die "Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n"; 407 } 408 if ($Options{propertieslisting} !~ /^(ByGroup|Alphabetical)$/i) { 409 die "Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n"; 410 } 411 if ($Options{quote} !~ /^(yes|no)$/i) { 412 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 413 } 414 } 415