1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: InfoNucleicAcids.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 "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Text::ParseWords; 34 use Benchmark; 35 use FileUtil; 36 use TextUtil; 37 use NucleicAcids; 38 39 my($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 ListNucleicAcidProperties(); 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 nucleic acid... 69 sub ListNucleicAcidData { 70 my($DataLabelRef, $DataValueRef) = @_; 71 my($Index, $Line, $Value); 72 73 if ($OptionsInfo{NucleicAcidRowsOutput}) { 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 "$Line\n"; 107 } 108 } 109 } 110 } 111 112 # List data for an nucleic acid... 113 sub ListHeaderRowData { 114 my($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 nucleic acids... 130 sub ListNucleicAcidProperties { 131 my($NucleicAcidID, $NucleicAcidDataRef, $PropertyName, $PropertyValue, @PropertyLabels, @PropertyValues); 132 133 print "Listing information for nucleic acid(s)...\n"; 134 135 if ($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{NucleicAcidRowsOutput}) { 147 ListHeaderRowData(\@PropertyLabels); 148 } 149 150 # Go over specified properties... 151 for $NucleicAcidID (@{$OptionsInfo{SpecifiedNucleicAcidIDs}}) { 152 $NucleicAcidDataRef = NucleicAcids::GetNucleicAcidPropertiesData($NucleicAcidID); 153 154 if (!$OptionsInfo{NucleicAcidRowsOutput}) { 155 if ($OptionsInfo{FileOutput}) { 156 print OUTFILE "\nListing properties for nucleic acid $NucleicAcidID...\n\n"; 157 } 158 else { 159 print "\nListing properties for nucleic acid $NucleicAcidID...\n\n"; 160 } 161 } 162 163 # Collect data.. 164 @PropertyValues = (); 165 for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) { 166 $PropertyValue = $NucleicAcidDataRef->{$PropertyName}; 167 if (IsFloat($PropertyValue)) { 168 $PropertyValue = sprintf("%.$OptionsInfo{Precision}f", $PropertyValue) + 0; 169 } 170 push @PropertyValues, $PropertyValue; 171 } 172 # List data... 173 ListNucleicAcidData(\@PropertyLabels, \@PropertyValues); 174 } 175 if ($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$/i) { 188 @PropertyNames = ('Code', 'OtherCodes', 'Name', 'Type', 'MolecularFormula', 'MolecularWeight'); 189 } elsif ($CategoryName =~ /^BasicPlus$/i) { 190 @PropertyNames = ('Code', 'OtherCodes', 'Name', 'Type', 'MolecularFormula', 'MolecularWeight', 'ExactMass', 'ElementalComposition'); 191 } 192 193 return @PropertyNames; 194 } 195 196 # Process option values... 197 sub ProcessOptions { 198 %OptionsInfo = (); 199 200 $OptionsInfo{Mode} = $Options{mode}; 201 202 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,"); 203 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0; 204 205 $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef; 206 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef; 207 208 $OptionsInfo{Output} = $Options{output}; 209 $OptionsInfo{OutputStyle} = $Options{outputstyle}; 210 211 $OptionsInfo{NucleicAcidRowsOutput} = ($Options{outputstyle} =~ /^NucleicAcidRows$/i) ? 1 : 0; 212 $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0; 213 214 $OptionsInfo{Precision} = $Options{precision}; 215 216 my($NucleicAcidID, @NucleicAcidIDs); 217 218 @{$OptionsInfo{SpecifiedNucleicAcidIDs}} = (); 219 220 # Set up Nucleic Acids IDs except for All mode... 221 @NucleicAcidIDs = (); 222 223 if (@ARGV >= 1) { 224 push @NucleicAcidIDs, @ARGV; 225 } 226 else { 227 # Setup mode specified default values... 228 if ($Options{mode} =~ /NucleicAcidID/i) { 229 push @NucleicAcidIDs, 'A'; 230 } 231 elsif ($Options{mode} =~ /NucleicAcidType/i) { 232 push @NucleicAcidIDs, 'Nucleoside'; 233 } 234 else { 235 push @NucleicAcidIDs, 'A'; 236 } 237 } 238 239 # Generate list of nucleic acids... 240 if (@ARGV == 1 && $ARGV[0] =~ /^All$/i) { 241 push @{$OptionsInfo{SpecifiedNucleicAcidIDs}}, NucleicAcids::GetNucleicAcids(); 242 } 243 else { 244 if ($Options{mode} =~ /NucleicAcidID/i) { 245 ID: for $NucleicAcidID (@NucleicAcidIDs) { 246 if (NucleicAcids::IsNucleicAcid($NucleicAcidID)) { 247 push @{$OptionsInfo{SpecifiedNucleicAcidIDs}}, $NucleicAcidID; 248 } 249 else { 250 warn "Ignoring nucleic acid ID, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid ID...\n"; 251 next ID; 252 } 253 } 254 } 255 elsif ($Options{mode} =~ /NucleicAcidType/i) { 256 ID: for $NucleicAcidID (@NucleicAcidIDs) { 257 if (!NucleicAcids::IsNucleicAcidType($NucleicAcidID)) { 258 warn "Ignoring nucleic acid type, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid type...\n"; 259 next ID; 260 } 261 push @{$OptionsInfo{SpecifiedNucleicAcidIDs}}, NucleicAcids::GetNucleicAcidsByType($NucleicAcidID); 262 } 263 } 264 } 265 SetupSpecifiedProperties(); 266 267 # Setup output file name... 268 $OptionsInfo{OutFileName} = ''; 269 if ($OptionsInfo{FileOutput}) { 270 my($OutFileRoot, $OutFileExt); 271 272 $OutFileRoot = ''; 273 $OutFileExt = "csv"; 274 if ($Options{outdelim} =~ /^tab$/i) { 275 $OutFileExt = "tsv"; 276 } 277 if ($Options{root}) { 278 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root}); 279 if ($RootFileName && $RootFileExt) { 280 $OutFileRoot = $RootFileName; 281 } 282 else { 283 $OutFileRoot = $Options{root}; 284 } 285 } 286 else { 287 $OutFileRoot = 'NucleicAcidsInfo'; 288 } 289 $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt; 290 if (!$Options{overwrite}) { 291 if (-e $OptionsInfo{OutFileName}) { 292 die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"; 293 } 294 } 295 } 296 } 297 298 # Setup properties to list... 299 sub SetupSpecifiedProperties { 300 301 $OptionsInfo{Properties} = defined $Options{properties} ? $Options{properties} : undef; 302 303 $OptionsInfo{PropertiesMode} = $Options{propertiesmode}; 304 $OptionsInfo{PropertiesListing} = $Options{propertieslisting}; 305 306 # Make sure appropriate properties/category names are specified... 307 @{$OptionsInfo{SpecifiedProperies}} = (); 308 if ($Options{properties} && ($Options{propertiesmode} =~ /^All$/i) ) { 309 warn "Warning: Ignoring values specifed by \"-p --properties\" option: Not valid for All value of \"--propertiesmode\" option...\n"; 310 } 311 if ($Options{propertiesmode} =~ /^All$/i) { 312 if ($Options{propertieslisting} =~ /^Alphabetical$/i) { 313 push @{$OptionsInfo{SpecifiedProperies}}, NucleicAcids::GetNucleicAcidPropertiesNames('Alphabetical'); 314 } 315 else { 316 push @{$OptionsInfo{SpecifiedProperies}}, NucleicAcids::GetNucleicAcidPropertiesNames(); 317 } 318 } 319 else { 320 if ($Options{properties}) { 321 if ($Options{propertiesmode} =~ /^Categories$/i) { 322 # Check category name... 323 if ($Options{properties} !~ /^(Basic|BasicPlus)$/i) { 324 die "Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic and BasicPlus\n"; 325 } 326 # Set propertynames... 327 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories($Options{properties}); 328 } 329 else { 330 # Check property names.. 331 my($Name, $PropertyName, @Names); 332 @Names = split /\,/, $Options{properties}; 333 NAME: for $Name (@Names) { 334 $PropertyName = RemoveLeadingAndTrailingWhiteSpaces($Name); 335 if (NucleicAcids::IsNucleicAcidProperty($PropertyName)) { 336 push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName; 337 } 338 else { 339 warn "Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n"; 340 } 341 } 342 if ($Options{propertieslisting} =~ /^Alphabetical$/i) { 343 # Code, OtherCodes and Name are always listed first... 344 my($CodePresent, $OtherCodesPresent, $NamePresent, @AlphabeticalProperties, %PropertiesMap); 345 %PropertiesMap = (); 346 @AlphabeticalProperties = (); 347 $CodePresent = 0; $OtherCodesPresent = 0; $NamePresent = 0; 348 NAME: for $Name (@{$OptionsInfo{SpecifiedProperies}}) { 349 if ($Name =~ /^Code$/i) { 350 $CodePresent = 1; 351 next NAME; 352 } 353 if ($Name =~ /^OtherCodes$/i) { 354 $OtherCodesPresent = 1; 355 next NAME; 356 } 357 if ($Name =~ /^Name$/i) { 358 $NamePresent = 1; 359 next NAME; 360 } 361 $PropertiesMap{$Name} = $Name; 362 } 363 # Setup the alphabetical list... 364 if ($CodePresent) { 365 push @AlphabeticalProperties, 'Code'; 366 } 367 if ($OtherCodesPresent) { 368 push @AlphabeticalProperties, 'OtherCodesPresent'; 369 } 370 if ($NamePresent) { 371 push @AlphabeticalProperties, 'Name'; 372 } 373 for $Name (sort keys %PropertiesMap) { 374 push @AlphabeticalProperties, $Name; 375 } 376 @{$OptionsInfo{SpecifiedProperies}} = (); 377 push @{$OptionsInfo{SpecifiedProperies}}, @AlphabeticalProperties; 378 } 379 } 380 } 381 else { 382 # Set default value... 383 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories('Basic'); 384 } 385 } 386 } 387 388 # Setup script usage and retrieve command line arguments specified using various options... 389 sub SetupScriptUsage { 390 391 # Retrieve all the options... 392 %Options = (); 393 $Options{mode} = "NucleicAcidID"; 394 $Options{outdelim} = "comma"; 395 $Options{output} = "STDOUT"; 396 $Options{outputstyle} = "NucleicAcidBlock"; 397 $Options{precision} = 4; 398 $Options{propertiesmode} = "Categories"; 399 $Options{propertieslisting} = "ByGroup"; 400 $Options{quote} = "yes"; 401 402 if (!GetOptions(\%Options, "help|h", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "properties|p=s", "propertieslisting=s", "propertiesmode=s", "quote|q=s", "root|r=s", "workingdir|w=s")) { 403 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 404 } 405 if ($Options{workingdir}) { 406 if (! -d $Options{workingdir}) { 407 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 408 } 409 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 410 } 411 if ($Options{mode} !~ /^(NucleicAcidID|NucleicAcidType)$/i) { 412 die "Error: The value specified, $Options{mode}, for option \"--mode\" is not valid. Allowed values: NucleicAcidID or NucleicAcidType\n"; 413 } 414 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 415 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 416 } 417 if ($Options{output} !~ /^(STDOUT|File)$/i) { 418 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"; 419 } 420 if ($Options{outputstyle} !~ /^(NucleicAcidBlock|NucleicAcidRows)$/i) { 421 die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: NucleicAcidBlock or NucleicAcidRows\n"; 422 } 423 if (!IsPositiveInteger($Options{precision})) { 424 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"; 425 } 426 if ($Options{propertiesmode} !~ /^(Categories|Names|All)$/i) { 427 die "Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n"; 428 } 429 if ($Options{propertieslisting} !~ /^(ByGroup|Alphabetical)$/i) { 430 die "Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n"; 431 } 432 if ($Options{quote} !~ /^(yes|no)$/i) { 433 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 434 } 435 } 436