1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: AnalyzeSequenceFilesData.pl,v $ 4 # $Date: 2015/02/28 20:46:04 $ 5 # $Revision: 1.33 $ 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 "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Text::ParseWords; 34 use Benchmark; 35 use FileUtil; 36 use TextUtil; 37 use SequenceFileUtil; 38 use AminoAcids; 39 use NucleicAcids; 40 41 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 42 43 # Autoflush STDOUT 44 $| = 1; 45 46 # Starting message... 47 $ScriptName = basename($0); 48 print "\n$ScriptName: Starting...\n\n"; 49 $StartTime = new Benchmark; 50 51 # Setup script usage message... 52 SetupScriptUsage(); 53 if ($Options{help} || @ARGV < 1) { 54 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 55 } 56 57 # Expand wild card file names... 58 my(@SequenceFilesList); 59 @SequenceFilesList = ExpandFileNames(\@ARGV, "aln msf fasta fta pir"); 60 61 print "Processing options...\n"; 62 my(%OptionsInfo); 63 ProcessOptions(); 64 65 # Set up information about input files... 66 print "Checking input sequence file(s)...\n"; 67 my(%SequenceFilesInfo); 68 RetrieveSequenceFilesInfo(); 69 SetupSequenceRegionsData(); 70 71 # Process input files.. 72 my($FileIndex); 73 if (@SequenceFilesList > 1) { 74 print "\nProcessing sequence files...\n"; 75 } 76 for $FileIndex (0 .. $#SequenceFilesList) { 77 if ($SequenceFilesInfo{FilesOkay}[$FileIndex]) { 78 print "\nProcessing file $SequenceFilesList[$FileIndex]...\n"; 79 AnalyzeSequenceFileData($FileIndex); 80 } 81 } 82 print "\n$ScriptName:Done...\n\n"; 83 84 $EndTime = new Benchmark; 85 $TotalTime = timediff ($EndTime, $StartTime); 86 print "Total time: ", timestr($TotalTime), "\n"; 87 88 ############################################################################### 89 90 # Analyze sequence file... 91 sub AnalyzeSequenceFileData { 92 my($FileIndex) = @_; 93 my($SequenceFile, $SequenceDataRef); 94 95 $SequenceFile = $SequenceFilesList[$FileIndex]; 96 97 open SEQUENCEFILE, "$SequenceFile" or die "Error: Can't open $SequenceFile: $! \n"; 98 $SequenceDataRef = ReadSequenceFile($SequenceFile); 99 close SEQUENCEFILE; 100 101 if ($OptionsInfo{CalculatePercentIdentityMatrix}) { 102 CalculatePercentIdentityMatrix($FileIndex, $SequenceDataRef); 103 } 104 if ($OptionsInfo{PerformResidueFrequencyAnalysis}) { 105 PerformResidueFrequencyAnalysis($FileIndex, $SequenceDataRef); 106 } 107 } 108 109 # Calculate percent identity matrix... 110 sub CalculatePercentIdentityMatrix { 111 my($FileIndex, $SequenceDataRef) = @_; 112 my($PercentIdentity, $PercentIdentityMatrixFile, $PercentIdentityMatrixRef, $RowID, $ColID, $Line, @LineWords); 113 114 $PercentIdentityMatrixFile = $SequenceFilesInfo{OutFileRoot}[$FileIndex] . 'PercentIdentityMatrix.' . $SequenceFilesInfo{OutFileExt}[$FileIndex]; 115 $PercentIdentityMatrixRef = CalculatePercentSequenceIdentityMatrix($SequenceDataRef, $OptionsInfo{IgnoreGaps}, $OptionsInfo{Precision}); 116 117 print "Generating percent identity matrix file $PercentIdentityMatrixFile...\n"; 118 open OUTFILE, ">$PercentIdentityMatrixFile" or die "Can't open $PercentIdentityMatrixFile: $!\n"; 119 120 # Write out column labels... 121 @LineWords = (); 122 push @LineWords, ''; 123 for $ColID (@{$PercentIdentityMatrixRef->{IDs}}) { 124 push @LineWords, $ColID; 125 } 126 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 127 print OUTFILE "$Line\n"; 128 129 # Write out rows... 130 for $RowID (@{$PercentIdentityMatrixRef->{IDs}}) { 131 @LineWords = (); 132 push @LineWords, $RowID; 133 for $ColID (@{$PercentIdentityMatrixRef->{IDs}}) { 134 $PercentIdentity = $PercentIdentityMatrixRef->{PercentIdentity}{$RowID}{$ColID}; 135 push @LineWords, $PercentIdentity; 136 } 137 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 138 print OUTFILE "$Line\n"; 139 } 140 close OUTFILE; 141 } 142 143 # Perform frequency analysis... 144 sub PerformResidueFrequencyAnalysis { 145 my($FileIndex, $SequenceDataRef) = @_; 146 147 CountResiduesInRegions($FileIndex, $SequenceDataRef); 148 CalculatePercentResidueFrequencyInRegions($FileIndex, $SequenceDataRef); 149 GeneratePercentResidueFrequencyOutFilesForRegions($FileIndex, $SequenceDataRef); 150 } 151 152 # Count residues... 153 sub CountResiduesInRegions { 154 my($FileIndex, $SequenceDataRef) = @_; 155 156 # Setup rerfernce sequence data... 157 my($RefereceSequenceID, $RefereceSequence); 158 $RefereceSequenceID = $SequenceFilesInfo{RefereceSequenceID}[$FileIndex]; 159 $RefereceSequence = $SequenceFilesInfo{RefereceSequence}[$FileIndex]; 160 161 # Count residues... 162 my($RegionID, $StartResNum, $EndResNum, $ResNum, $ResIndex, $ID, $Sequence, $Residue); 163 for $RegionID (@{$SequenceFilesInfo{RegionsData}[$FileIndex]{RegionIDs}}) { 164 $StartResNum = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{StartResNum}; 165 $EndResNum = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{EndResNum}; 166 RESNUM: for $ResNum ($StartResNum .. $EndResNum) { 167 $ResIndex = $ResNum - 1; 168 if ($OptionsInfo{IgnoreGaps} && $SequenceFilesInfo{RefereceSequenceResNums}[$FileIndex]{IsGap}{$ResNum}) { 169 next RESNUM; 170 } 171 # Go over residues in column $ResNum in all the sequences... 172 ID: for $ID (@{$SequenceDataRef->{IDs}}) { 173 $Sequence = $SequenceDataRef->{Sequence}{$ID}; 174 $Residue = substr($Sequence, $ResIndex, 1); 175 if (IsGapResidue($Residue)) { 176 $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{Count}{$ResNum}{Gap} += 1; 177 } 178 else { 179 if (exists $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{Count}{$ResNum}{$Residue}) { 180 $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{Count}{$ResNum}{$Residue} += 1; 181 } 182 else { 183 # Internal error... 184 print "Warning: Ignoring residue $Residue in sequence $ID during ResidueFrequencyAnalysis calculation: Unknown residue...\n"; 185 } 186 } 187 } 188 } 189 } 190 } 191 192 # Calculate percent frequency for various residues in the sequence regions... 193 sub CalculatePercentResidueFrequencyInRegions { 194 my($FileIndex, $SequenceDataRef) = @_; 195 my($RegionID, $StartResNum, $EndResNum, $ResNum, $Residue, $Count, $PercentCount, $MaxResiduesCount, $Precision); 196 197 $MaxResiduesCount = $SequenceDataRef->{Count}; 198 $Precision = $OptionsInfo{Precision}; 199 for $RegionID (@{$SequenceFilesInfo{RegionsData}[$FileIndex]{RegionIDs}}) { 200 $StartResNum = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{StartResNum}; 201 $EndResNum = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{EndResNum}; 202 RESNUM: for $ResNum ($StartResNum .. $EndResNum) { 203 if ($OptionsInfo{IgnoreGaps} && $SequenceFilesInfo{RefereceSequenceResNums}[$FileIndex]{IsGap}{$ResNum}) { 204 next RESNUM; 205 } 206 for $Residue (keys %{$SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{Count}{$ResNum}}) { 207 $Count = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{Count}{$ResNum}{$Residue}; 208 $PercentCount = ($Count / $MaxResiduesCount) * 100; 209 $PercentCount = sprintf("%.${Precision}f", $PercentCount) + 0; 210 $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{PercentCount}{$ResNum}{$Residue} = $PercentCount; 211 } 212 } 213 } 214 } 215 216 # Generate output files... 217 sub GeneratePercentResidueFrequencyOutFilesForRegions { 218 my($FileIndex, $SequenceDataRef) = @_; 219 220 # Setup rerfernce sequence data... 221 my($RefereceSequenceID, $RefereceSequence); 222 $RefereceSequenceID = $SequenceFilesInfo{RefereceSequenceID}[$FileIndex]; 223 $RefereceSequence = $SequenceFilesInfo{RefereceSequence}[$FileIndex]; 224 225 my($RegionID, $StartResNum, $EndResNum, $ResNum, $Count, $PercentCount, $Residue, $RegionNum, $RegionOutFile, $PercentRegionOutFile, $OutFileRoot, $OutFileExt, $Line, @LineWords, @PercentLineWords); 226 227 $OutFileRoot = $SequenceFilesInfo{OutFileRoot}[$FileIndex]; 228 $OutFileExt = $SequenceFilesInfo{OutFileExt}[$FileIndex]; 229 $RegionNum = 0; 230 for $RegionID (@{$SequenceFilesInfo{RegionsData}[$FileIndex]{RegionIDs}}) { 231 $RegionNum++; 232 $StartResNum = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{StartResNum}; 233 $EndResNum = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{EndResNum}; 234 235 $RegionOutFile = "${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"; 236 $PercentRegionOutFile = "${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"; 237 238 print "Generating $RegionOutFile and $PercentRegionOutFile...\n"; 239 open REGIONOUTFILE, ">$RegionOutFile" or die "Error: Can't open $RegionOutFile: $! \n"; 240 open PERCENTREGIONOUTFILE, ">$PercentRegionOutFile" or die "Error: Can't open $PercentRegionOutFile: $! \n"; 241 242 # Write out reference residue positions as column values.... 243 @LineWords = (); 244 push @LineWords, ''; 245 RESNUM: for $ResNum ($StartResNum .. $EndResNum) { 246 if ($OptionsInfo{IgnoreGaps} && $SequenceFilesInfo{RefereceSequenceResNums}[$FileIndex]{IsGap}{$ResNum}) { 247 next RESNUM; 248 } 249 push @LineWords, $ResNum; 250 } 251 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 252 print REGIONOUTFILE "$Line\n"; 253 print PERCENTREGIONOUTFILE "$Line\n"; 254 255 256 # Write out row data for each residue; Gap residue is written last... 257 RESIDUE: for $Residue (sort @{$SequenceFilesInfo{ResidueCodes}[$FileIndex]}) { 258 if ($Residue =~ /^Gap$/i) { 259 next RESIDUE; 260 } 261 @LineWords = (); 262 push @LineWords, $Residue; 263 @PercentLineWords = (); 264 push @PercentLineWords, $Residue; 265 266 RESNUM: for $ResNum ($StartResNum .. $EndResNum) { 267 if ($OptionsInfo{IgnoreGaps} && $SequenceFilesInfo{RefereceSequenceResNums}[$FileIndex]{IsGap}{$ResNum}) { 268 next RESNUM; 269 } 270 $Count = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{Count}{$ResNum}{$Residue}; 271 push @LineWords, $Count; 272 $PercentCount = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{PercentCount}{$ResNum}{$Residue}; 273 push @PercentLineWords, $PercentCount; 274 } 275 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 276 print REGIONOUTFILE "$Line\n"; 277 278 $Line = JoinWords(\@PercentLineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 279 print PERCENTREGIONOUTFILE "$Line\n"; 280 } 281 282 # Write out data for gap... 283 $Residue = 'Gap'; 284 @LineWords = (); 285 push @LineWords, $Residue; 286 @PercentLineWords = (); 287 push @PercentLineWords, $Residue; 288 289 RESNUM: for $ResNum ($StartResNum .. $EndResNum) { 290 if ($OptionsInfo{IgnoreGaps} && $SequenceFilesInfo{RefereceSequenceResNums}[$FileIndex]{IsGap}{$ResNum}) { 291 next RESNUM; 292 } 293 $Count = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{Count}{$ResNum}{$Residue}; 294 push @LineWords, $Count; 295 296 $PercentCount = $SequenceFilesInfo{RegionsData}[$FileIndex]{$RegionID}{PercentCount}{$ResNum}{$Residue}; 297 push @PercentLineWords, $PercentCount; 298 } 299 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 300 print REGIONOUTFILE "$Line\n"; 301 302 $Line = JoinWords(\@PercentLineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 303 print PERCENTREGIONOUTFILE "$Line\n"; 304 305 close REGIONOUTFILE; 306 close PERCENTREGIONOUTFILE; 307 } 308 } 309 310 # Process option values... 311 sub ProcessOptions { 312 %OptionsInfo = (); 313 314 # Setup analysis mode... 315 $OptionsInfo{CalculatePercentIdentityMatrix} = ($Options{mode} =~ /^(PercentIdentityMatrix|All)$/i) ? 1 : 0; 316 $OptionsInfo{PerformResidueFrequencyAnalysis} = ($Options{mode} =~ /^(ResidueFrequencyAnalysis|All)$/i) ? 1 : 0; 317 318 # Setup delimiter and quotes... 319 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /tab/i ) ? "\t" : (($Options{outdelim} =~ /semicolon/i) ? "\;" : "\,"); 320 $OptionsInfo{OutQuote} = ($Options{quote} =~ /yes/i ) ? 1 : 0; 321 322 # Setup reference sequence and regions for residue frequence analysis... 323 $OptionsInfo{SpecifiedRefereceSequence} = $Options{referencesequence}; 324 $OptionsInfo{SpecifiedRegion} = $Options{region}; 325 @{$OptionsInfo{SpecifiedRegions}} = (); 326 327 my(@SpecifiedRegions); 328 @SpecifiedRegions = (); 329 if ($Options{region} =~ /\,/) { 330 @SpecifiedRegions = split /\,/, $OptionsInfo{SpecifiedRegion}; 331 if (@SpecifiedRegions % 2) { 332 die "Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"; 333 } 334 # Make sure EndResNum > StartResNum... 335 my($StartResNum, $EndResNum, $Index, $RegionNum); 336 $RegionNum = 0; 337 for ($Index = 0; $Index <= $#SpecifiedRegions; $Index += 2) { 338 $StartResNum = $SpecifiedRegions[$Index]; 339 $EndResNum = $SpecifiedRegions[$Index + 1]; 340 $RegionNum++; 341 if (!IsPositiveInteger($StartResNum)) { 342 die "Error: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be a positive integer for region $RegionNum.\n"; 343 } 344 if (!IsPositiveInteger($EndResNum)) { 345 die "Error: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $EndResNum, must be a positive integer for region $RegionNum.\n"; 346 } 347 if ($StartResNum >= $EndResNum) { 348 die "Error: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be smaller than end residue number, $EndResNum, for region $RegionNum.\n"; 349 } 350 } 351 } 352 else { 353 if ($Options{region} !~ /^UseCompleteSequence$/i) { 354 die "Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"; 355 } 356 } 357 push @{$OptionsInfo{SpecifiedRegions}}, @SpecifiedRegions; 358 359 # Miscellaneous options... 360 $OptionsInfo{Precision} = $Options{precision}; 361 $OptionsInfo{IgnoreGaps} = ($Options{ignoregaps} =~ /Yes/i) ? 1 : 0; 362 $OptionsInfo{RegionResiduesMode} = $Options{regionresiduesmode}; 363 364 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; 365 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; 366 } 367 368 # Retrieve information about sequence files... 369 sub RetrieveSequenceFilesInfo { 370 my($Index, $SequenceFile, $FileSupported, $FileFormat, $SequenceCount, $RefereceSequence, $RefereceSequenceID, $RefereceSequenceLen, $RefereceSequenceWithNoGaps, $RefereceSequenceWithNoGapsLen, $RefereceSequenceRegionCount, $FileDir, $FileName, $FileExt, $OutFileRoot, $OutFileExt, $SequenceDataRef, $SpecifiedRefereceSequence, @SpecifiedRegions, @RefereceSequenceRegions); 371 372 %SequenceFilesInfo = (); 373 @{$SequenceFilesInfo{FilesOkay}} = (); 374 @{$SequenceFilesInfo{OutFileRoot}} = (); 375 @{$SequenceFilesInfo{OutFileExt}} = (); 376 @{$SequenceFilesInfo{Format}} = (); 377 @{$SequenceFilesInfo{SequenceCount}} = (); 378 @{$SequenceFilesInfo{RefereceSequenceID}} = (); 379 @{$SequenceFilesInfo{RefereceSequence}} = (); 380 @{$SequenceFilesInfo{RefereceSequenceLen}} = (); 381 @{$SequenceFilesInfo{RefereceSequenceWithNoGaps}} = (); 382 @{$SequenceFilesInfo{RefereceSequenceWithNoGapsLen}} = (); 383 @{$SequenceFilesInfo{RefereceSequenceRegions}} = (); 384 @{$SequenceFilesInfo{RefereceSequenceRegionCount}} = (); 385 @{$SequenceFilesInfo{ResidueCodes}} = (); 386 387 FILELIST: for $Index (0 .. $#SequenceFilesList) { 388 $SequenceFile = $SequenceFilesList[$Index]; 389 $SequenceFilesInfo{FilesOkay}[$Index] = 0; 390 $SequenceFilesInfo{OutFileRoot}[$Index] = ''; 391 $SequenceFilesInfo{OutFileExt}[$Index] = ''; 392 $SequenceFilesInfo{Format}[$Index] = 'NotSupported'; 393 $SequenceFilesInfo{SequenceCount}[$Index] = 0; 394 $SequenceFilesInfo{RefereceSequenceID}[$Index] = ''; 395 $SequenceFilesInfo{RefereceSequence}[$Index] = ''; 396 $SequenceFilesInfo{RefereceSequenceLen}[$Index] = ''; 397 $SequenceFilesInfo{RefereceSequenceWithNoGaps}[$Index] = ''; 398 $SequenceFilesInfo{RefereceSequenceWithNoGapsLen}[$Index] = ''; 399 @{$SequenceFilesInfo{RefereceSequenceRegions}[$Index]} = (); 400 $SequenceFilesInfo{RefereceSequenceRegionCount}[$Index] = 0; 401 @{$SequenceFilesInfo{ResidueCodes}[$Index]} = (); 402 403 if (! open SEQUENCEFILE, "$SequenceFile") { 404 warn "Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n"; 405 next FILELIST; 406 } 407 close SEQUENCEFILE; 408 409 ($FileSupported, $FileFormat) = IsSupportedSequenceFile($SequenceFile); 410 if (!$FileSupported) { 411 warn "Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n"; 412 next FILELIST; 413 } 414 415 $SequenceDataRef = ReadSequenceFile($SequenceFile); 416 417 $SequenceCount = $SequenceDataRef->{Count}; 418 if (!$SequenceCount) { 419 warn "Warning: Ignoring file $SequenceFile: Sequence data is missing.\n"; 420 next FILELIST; 421 } 422 423 # Make sure all sequence lengths are identical... 424 if (!AreSequenceLengthsIdentical($SequenceDataRef)) { 425 warn "Warning: Ignoring file $SequenceFile: Sequence legths are not identical.\n"; 426 next FILELIST; 427 } 428 $SpecifiedRefereceSequence = $OptionsInfo{SpecifiedRefereceSequence}; 429 # Make sure reference sequence ID is valid... 430 if ($SpecifiedRefereceSequence =~ /^UseFirstSequenceID$/i) { 431 $RefereceSequenceID = $SequenceDataRef->{IDs}[0]; 432 } 433 else { 434 if (!exists($SequenceDataRef->{Sequence}{$SpecifiedRefereceSequence})) { 435 warn "Warning: Ignoring file $SequenceFile: Rreference sequence ID, $SpecifiedRefereceSequence, specified using option \"--referencesequence\" is missing.\n"; 436 next FILELIST; 437 } 438 $RefereceSequenceID = $SpecifiedRefereceSequence; 439 } 440 441 # Make sure sequence regions corresponding to reference sequence are valid... 442 @RefereceSequenceRegions = (); 443 $RefereceSequenceRegionCount = 0; 444 $RefereceSequence = $SequenceDataRef->{Sequence}{$RefereceSequenceID}; 445 $RefereceSequenceLen = length $RefereceSequence; 446 447 $RefereceSequenceWithNoGaps = RemoveSequenceGaps($RefereceSequence); 448 $RefereceSequenceWithNoGapsLen = length $RefereceSequenceWithNoGaps; 449 450 @SpecifiedRegions = (); 451 push @SpecifiedRegions, @{$OptionsInfo{SpecifiedRegions}}; 452 if (@SpecifiedRegions) { 453 # Make sure specified regions are valid... 454 my($StartResNum, $EndResNum, $RegionIndex, $RegionNum); 455 $RegionNum = 0; 456 for ($RegionIndex = 0; $RegionIndex <= $#SpecifiedRegions; $RegionIndex += 2) { 457 $StartResNum = $SpecifiedRegions[$RegionIndex]; 458 $EndResNum = $SpecifiedRegions[$RegionIndex + 1]; 459 $RegionNum++; 460 if ($OptionsInfo{IgnoreGaps}) { 461 if ($StartResNum > $RefereceSequenceWithNoGapsLen) { 462 warn "Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be smaller the sequence length, $RefereceSequenceWithNoGapsLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"; 463 next FILELIST; 464 } 465 if ($EndResNum > $RefereceSequenceWithNoGapsLen) { 466 warn "Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The end residue number, $EndResNum, must be smaller the sequence length, $RefereceSequenceWithNoGapsLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"; 467 next FILELIST; 468 } 469 } 470 else { 471 if ($StartResNum > $RefereceSequenceLen) { 472 warn "Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be smaller the sequence length, $RefereceSequenceLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum.\n"; 473 next FILELIST; 474 } 475 if ($EndResNum > $RefereceSequenceLen) { 476 warn "Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The end residue number, $EndResNum, must be smaller the sequence length, $RefereceSequenceLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum.\n"; 477 next FILELIST; 478 } 479 } 480 push @RefereceSequenceRegions, ($StartResNum, $EndResNum); 481 } 482 $RefereceSequenceRegionCount = $RegionNum; 483 } 484 else { 485 # Use complete sequence corresponding to reference sequence ID... 486 if ($OptionsInfo{IgnoreGaps}) { 487 push @RefereceSequenceRegions, (1, $RefereceSequenceWithNoGapsLen); 488 } 489 else { 490 push @RefereceSequenceRegions, (1, $RefereceSequenceLen); 491 } 492 $RefereceSequenceRegionCount = 1; 493 } 494 # Setup output file names... 495 $FileDir = ""; $FileName = ""; $FileExt = ""; 496 ($FileDir, $FileName, $FileExt) = ParseFileName($SequenceFile); 497 $FileExt = "csv"; 498 if ($Options{outdelim} =~ /^tab$/i) { 499 $FileExt = "tsv"; 500 } 501 $OutFileExt = $FileExt; 502 if ($OptionsInfo{OutFileRoot} && (@SequenceFilesList == 1)) { 503 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); 504 if ($RootFileName && $RootFileExt) { 505 $FileName = $RootFileName; 506 } 507 else { 508 $FileName = $OptionsInfo{OutFileRoot}; 509 } 510 $OutFileRoot = $FileName; 511 } 512 else { 513 $OutFileRoot = $FileName; 514 } 515 if (!$OptionsInfo{OverwriteFiles}) { 516 if ($OptionsInfo{CalculatePercentIdentityMatrix}) { 517 if (-e "${OutFileRoot}PercentIdentityMatrix.${OutFileExt}") { 518 warn "Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}PercentIdentityMatrix.${OutFileExt} already exists\n"; 519 next FILELIST; 520 } 521 } 522 if ($OptionsInfo{PerformResidueFrequencyAnalysis}) { 523 my($RegionNum); 524 for $RegionNum (1 .. $RefereceSequenceRegionCount) { 525 if (-e "${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}") { 526 warn "Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"; 527 next FILELIST; 528 } 529 if (-e "${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}") { 530 warn "Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"; 531 next FILELIST; 532 } 533 } 534 } 535 } 536 537 $SequenceFilesInfo{FilesOkay}[$Index] = 1; 538 $SequenceFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; 539 $SequenceFilesInfo{OutFileExt}[$Index] = $OutFileExt; 540 541 $SequenceFilesInfo{Format}[$Index] = $FileFormat; 542 $SequenceFilesInfo{SequenceCount}[$Index] = $SequenceCount; 543 $SequenceFilesInfo{RefereceSequenceID}[$Index] = $RefereceSequenceID; 544 $SequenceFilesInfo{RefereceSequence}[$Index] = $RefereceSequence; 545 $SequenceFilesInfo{RefereceSequenceLen}[$Index] = $RefereceSequenceLen; 546 $SequenceFilesInfo{RefereceSequenceWithNoGaps}[$Index] = $RefereceSequenceWithNoGaps; 547 $SequenceFilesInfo{RefereceSequenceWithNoGapsLen}[$Index] = $RefereceSequenceWithNoGapsLen; 548 push @{$SequenceFilesInfo{RefereceSequenceRegions}[$Index]}, @RefereceSequenceRegions; 549 $SequenceFilesInfo{RefereceSequenceRegionCount}[$Index] = $RefereceSequenceRegionCount; 550 551 # Setup residue codes... 552 SetupSequenceFileResidueCodes($SequenceDataRef, $Index); 553 } 554 } 555 556 sub SetupSequenceFileResidueCodes { 557 my($SequenceDataRef, $FileIndex) = @_; 558 my($Residue, @ResidueCodesList, %ResidueCodesMap); 559 560 # Initialize 561 @{$SequenceFilesInfo{ResidueCodes}[$FileIndex]} = (); 562 563 %ResidueCodesMap = (); 564 @ResidueCodesList = (); 565 566 # Setup standard amino acids and nucleic acids one letter codes... 567 if ($OptionsInfo{RegionResiduesMode} =~ /^AminoAcids$/i) { 568 @ResidueCodesList = AminoAcids::GetAminoAcids('OneLetterCode'); 569 } 570 elsif ($OptionsInfo{RegionResiduesMode} =~ /^NucleicAcids$/i) { 571 push @ResidueCodesList, ('A', 'G', 'T', 'U', 'C'); 572 } 573 push @ResidueCodesList, 'Gap'; 574 for $Residue (@ResidueCodesList) { 575 $ResidueCodesMap{$Residue} = $Residue; 576 } 577 578 # Go over all the residues in all the sequences and add missing ones to the list... 579 my($ID, $Sequence, $ResIndex); 580 for $ID (@{$SequenceDataRef->{IDs}}) { 581 $Sequence = $SequenceDataRef->{Sequence}{$ID}; 582 RES: for $ResIndex (0 .. (length($Sequence) - 1)) { 583 $Residue = substr($Sequence, $ResIndex, 1); 584 if (IsGapResidue($Residue)) { 585 next RES; 586 } 587 if (exists $ResidueCodesMap{$Residue}) { 588 next RES; 589 } 590 push @ResidueCodesList, $Residue; 591 $ResidueCodesMap{$Residue} = $Residue; 592 } 593 } 594 push @{$SequenceFilesInfo{ResidueCodes}[$FileIndex]}, @ResidueCodesList; 595 } 596 597 # Setup regions data for performing residue frequency analysis... 598 sub SetupSequenceRegionsData { 599 my($Index, $RefereceSequence, $RefereceSequenceLen, $RegionID, $StartResNum, $EndResNum, $RegionIndex, $RegionNum, $NoGapResNum, $ResNum, $ResIndex, $Residue, $ResidueCode, @RefereceSequenceRegions); 600 601 602 @{$SequenceFilesInfo{RefereceSequenceResNums}} = (); 603 @{$SequenceFilesInfo{RegionsData}} = (); 604 605 FILELIST: for $Index (0 .. $#SequenceFilesList) { 606 %{$SequenceFilesInfo{RefereceSequenceResNums}[$Index]{IsGap}} = (); 607 %{$SequenceFilesInfo{RefereceSequenceResNums}[$Index]{NoGapToGap}} = (); 608 %{$SequenceFilesInfo{RefereceSequenceResNums}[$Index]{GapToNoGap}} = (); 609 %{$SequenceFilesInfo{RegionsData}[$Index]} = (); 610 @{$SequenceFilesInfo{RegionsData}[$Index]{RegionIDs}} = (); 611 612 if (!$SequenceFilesInfo{FilesOkay}[$Index]) { 613 next FILELIST; 614 } 615 if (!$OptionsInfo{PerformResidueFrequencyAnalysis}) { 616 next FILELIST; 617 } 618 619 $RefereceSequence = $SequenceFilesInfo{RefereceSequence}[$Index]; 620 $RefereceSequenceLen = $SequenceFilesInfo{RefereceSequenceLen}[$Index]; 621 622 # Setup residue number mapping and gap status for refernece sequence... 623 $NoGapResNum = 0; 624 $ResNum = 0; 625 for $ResIndex (0 .. ($RefereceSequenceLen - 1)) { 626 $ResNum++; 627 $Residue = substr($RefereceSequence, $ResIndex, 1); 628 $SequenceFilesInfo{RefereceSequenceResNums}[$Index]{IsGap}{$ResNum} = 1; 629 if (!IsGapResidue($Residue)) { 630 $NoGapResNum++; 631 $SequenceFilesInfo{RefereceSequenceResNums}[$Index]{IsGap}{$ResNum} = 0; 632 $SequenceFilesInfo{RefereceSequenceResNums}[$Index]{NoGapToGap}{$NoGapResNum} = $ResNum; 633 $SequenceFilesInfo{RefereceSequenceResNums}[$Index]{GapToNoGap}{$ResNum} = $NoGapResNum; 634 } 635 } 636 # Map residue numbers for specified regions to the reference residue in input sequence/alignment files 637 $RegionNum = 0; 638 @RefereceSequenceRegions = (); 639 push @RefereceSequenceRegions, @{$SequenceFilesInfo{RefereceSequenceRegions}[$Index]}; 640 for ($RegionIndex = 0; $RegionIndex <= $#RefereceSequenceRegions; $RegionIndex += 2) { 641 $StartResNum = $RefereceSequenceRegions[$RegionIndex]; 642 $EndResNum = $RefereceSequenceRegions[$RegionIndex + 1]; 643 $RegionNum++; 644 $RegionID = "Region${RegionNum}"; 645 if ($OptionsInfo{IgnoreGaps}) { 646 # Map residue numbers to the reference sequence residue numbers to account for any ignored gaps... 647 $StartResNum = $SequenceFilesInfo{RefereceSequenceResNums}[$Index]{NoGapToGap}{$StartResNum}; 648 $EndResNum = $SequenceFilesInfo{RefereceSequenceResNums}[$Index]{NoGapToGap}{$EndResNum}; 649 } 650 push @{$SequenceFilesInfo{RegionsData}[$Index]{RegionIDs}}, $RegionID; 651 $SequenceFilesInfo{RegionsData}[$Index]{$RegionID}{StartResNum} = $StartResNum; 652 $SequenceFilesInfo{RegionsData}[$Index]{$RegionID}{EndResNum} = $EndResNum; 653 654 # Initialize data for residue codes... 655 for $ResNum ($StartResNum .. $EndResNum) { 656 for $ResidueCode (@{$SequenceFilesInfo{ResidueCodes}[$Index]}) { 657 $SequenceFilesInfo{RegionsData}[$Index]{$RegionID}{Count}{$ResNum}{$ResidueCode} = 0; 658 } 659 } 660 } 661 } 662 } 663 664 # Setup script usage and retrieve command line arguments specified using various options... 665 sub SetupScriptUsage { 666 667 # Retrieve all the options... 668 %Options = (); 669 $Options{ignoregaps} = 'yes'; 670 $Options{regionresiduesmode} = 'None'; 671 $Options{mode} = 'PercentIdentityMatrix'; 672 $Options{outdelim} = 'comma'; 673 $Options{precision} = 2; 674 $Options{quote} = 'yes'; 675 $Options{referencesequence} = 'UseFirstSequenceID'; 676 $Options{region} = 'UseCompleteSequence'; 677 678 if (!GetOptions(\%Options, "help|h", "ignoregaps|i=s", "mode|m=s", "outdelim=s", "overwrite|o", "precision|p=i", "quote|q=s", "referencesequence=s", "region=s", "regionresiduesmode=s", "root|r=s", "workingdir|w=s")) { 679 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 680 } 681 if ($Options{workingdir}) { 682 if (! -d $Options{workingdir}) { 683 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 684 } 685 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 686 } 687 if ($Options{ignoregaps} !~ /^(yes|no)$/i) { 688 die "Error: The value specified, $Options{ignoregaps}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 689 } 690 if ($Options{regionresiduesmode} !~ /^(AminoAcids|NucleicAcids|None)$/i) { 691 die "Error: The value specified, $Options{regionresiduesmode}, for option \"--regionresiduesmode\" is not valid. Allowed values: AminoAcids, NucleicAcids or None\n"; 692 } 693 if ($Options{mode} !~ /^(PercentIdentityMatrix|ResidueFrequencyAnalysis|All)$/i) { 694 die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: PercentIdentityMatrix, ResidueFrequencyAnalysis or All\n"; 695 } 696 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 697 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 698 } 699 if ($Options{quote} !~ /^(yes|no)$/i) { 700 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 701 } 702 if (!IsPositiveInteger($Options{precision})) { 703 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"; 704 } 705 } 706