1# 2# BioPerl module for Bio::Tools::Run::Alignment::Kalign 3# 4# Please direct questions and support issues to <bioperl-l@bioperl.org> 5# 6# Cared for by Albert Vilella 7# 8# Copyright Albert Vilella 9# 10# You may distribute this module under the same terms as perl itself 11# 12# POD documentation - main docs before the code 13 14=head1 NAME 15 16Bio::Tools::Run::Alignment::Kalign - Object for the calculation of an 17iterative multiple sequence alignment from a set of unaligned 18sequences or alignments using the KALIGN program 19 20=head1 SYNOPSIS 21 22 # Build a kalign alignment factory 23 $factory = Bio::Tools::Run::Alignment::Kalign->new(@params); 24 25 # Pass the factory a list of sequences to be aligned. 26 $inputfilename = 't/cysprot.fa'; 27 # $aln is a SimpleAlign object. 28 $aln = $factory->align($inputfilename); 29 30 # or where @seq_array is an array of Bio::Seq objects 31 $seq_array_ref = \@seq_array; 32 $aln = $factory->align($seq_array_ref); 33 34 # Or one can pass the factory a pair of (sub)alignments 35 #to be aligned against each other, e.g.: 36 37 #There are various additional options and input formats available. 38 #See the DESCRIPTION section that follows for additional details. 39 40=head1 DESCRIPTION 41 42Please cite: 43 44 Timo Lassmann and Erik L.L. Sonnhammer (2005) 45 Kalign - an accurate and fast multiple sequence alignment algorithm. 46 BMC Bioinformatics 6:298 47 48http://msa.cgb.ki.se/downloads/kalign/current.tar.gz 49 50 51=head2 Helping the module find your executable 52 53You will need to enable Kalign to find the kalign program. This can be 54done in (at least) three ways: 55 56 1. Make sure the kalign executable is in your path (i.e. 57 'which kalign' returns a valid program 58 2. define an environmental variable KALIGNDIR which points to a 59 directory containing the 'kalign' app: 60 In bash 61 export KALIGNDIR=/home/progs/kalign or 62 In csh/tcsh 63 setenv KALIGNDIR /home/progs/kalign 64 65 3. include a definition of an environmental variable KALIGNDIR 66 in every script that will 67 BEGIN {$ENV{KALIGNDIR} = '/home/progs/kalign'; } 68 use Bio::Tools::Run::Alignment::Kalign; 69 70=head1 FEEDBACK 71 72=head2 Mailing Lists 73 74User feedback is an integral part of the evolution of this and other 75Bioperl modules. Send your comments and suggestions preferably to one 76of the Bioperl mailing lists. Your participation is much appreciated. 77 78 bioperl-l@bioperl.org - General discussion 79 http://bioperl.org/wiki/Mailing_lists - About the mailing lists 80 81=head2 Support 82 83Please direct usage questions or support issues to the mailing list: 84 85I<bioperl-l@bioperl.org> 86 87rather than to the module maintainer directly. Many experienced and 88reponsive experts will be able look at the problem and quickly 89address it. Please include a thorough description of the problem 90with code and data examples if at all possible. 91 92=head2 Reporting Bugs 93 94Report bugs to the Bioperl bug tracking system to help us keep track 95the bugs and their resolution. Bug reports can be submitted via the web: 96 97 http://redmine.open-bio.org/projects/bioperl/ 98 99=head1 AUTHOR - Albert Vilella 100 101Email idontlikespam@hotmail.com 102 103=head1 APPENDIX 104 105The rest of the documentation details each of the object 106methods. Internal methods are usually preceded with a _ 107 108=cut 109 110package Bio::Tools::Run::Alignment::Kalign; 111 112use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS 113 @KALIGN_PARAMS @KALIGN_SWITCHES %OK_FIELD 114 ); 115use strict; 116use Bio::Seq; 117use Bio::SeqIO; 118use Bio::SimpleAlign; 119use Bio::AlignIO; 120use Bio::Root::Root; 121use Bio::Root::IO; 122use Bio::Factory::ApplicationFactoryI; 123use Bio::Tools::Run::WrapperBase; 124@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase 125 Bio::Factory::ApplicationFactoryI); 126 127 128BEGIN { 129 %DEFAULTS = ( 'AFORMAT' => 'fasta' ); 130 @KALIGN_PARAMS = qw(IN OUT GAPOPEN GAPEXTENSION TERMINAL_GAP_EXTENSION_PENALTY MATRIX_BONUS 131 SORT FEATURE DISTANCE TREE ZCUTOFF FORMAT 132 MAXMB MAXHOURS MAXITERS); 133 @KALIGN_SWITCHES = qw(QUIET); 134 135# Authorize attribute fields 136 foreach my $attr ( @KALIGN_PARAMS, @KALIGN_SWITCHES ) { 137 $OK_FIELD{$attr}++; } 138} 139 140=head2 program_name 141 142 Title : program_name 143 Usage : $factory->program_name() 144 Function: holds the program name 145 Returns: string 146 Args : None 147 148=cut 149 150sub program_name { 151 return 'kalign'; 152} 153 154=head2 program_dir 155 156 Title : program_dir 157 Usage : $factory->program_dir(@params) 158 Function: returns the program directory, obtained from ENV variable. 159 Returns: string 160 Args : 161 162=cut 163 164sub program_dir { 165 return Bio::Root::IO->catfile($ENV{KALIGNDIR}) if $ENV{KALIGNDIR}; 166} 167 168=head2 new 169 170 Title : new 171 Usage : my $kalign = Bio::Tools::Run::Alignment::Kalign->new(); 172 Function: Constructor 173 Returns : Bio::Tools::Run::Alignment::Kalign 174 Args : -outfile_name => $outname 175 176 177=cut 178 179sub new { 180 my ($class,@args) = @_; 181 my( @kalign_args, @obj_args); 182 while( my $arg = shift @args ) { 183 if( $arg =~ /^-/ ) { 184 push @obj_args, $arg, shift @args; 185 } else { 186 push @kalign_args,$arg, shift @args; 187 } 188 } 189 my $self = $class->SUPER::new(@obj_args); 190 191 my ($on) = $self->_rearrange([qw(OUTFILE_NAME)],@obj_args); 192 193 $self->outfile_name($on || ''); 194 my ($attr, $value); 195 # FIXME: only tested with fasta output format right now... 196 $self->aformat($DEFAULTS{'AFORMAT'}); 197 198 while ( @kalign_args) { 199 $attr = shift @kalign_args; 200 $value = shift @kalign_args; 201 next if( $attr =~ /^-/); # don't want named parameters 202 $self->$attr($value); 203 } 204 205 if( defined $self->out ) { 206 $self->outfile_name($self->out); 207 } 208 return $self; 209} 210 211sub AUTOLOAD { 212 my $self = shift; 213 my $attr = $AUTOLOAD; 214 $attr =~ s/.*:://; 215 $attr = uc $attr; 216 # aliasing 217 $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr}; 218 219 $self->{$attr} = shift if @_; 220 return $self->{$attr}; 221} 222 223=head2 error_string 224 225 Title : error_string 226 Usage : $obj->error_string($newval) 227 Function: Where the output from the last analysus run is stored. 228 Returns : value of error_string 229 Args : newvalue (optional) 230 231 232=cut 233 234sub error_string{ 235 my ($self,$value) = @_; 236 if( defined $value) { 237 $self->{'error_string'} = $value; 238 } 239 return $self->{'error_string'}; 240 241} 242 243=head2 version 244 245 Title : version 246 Usage : exit if $prog->version() < 2 247 Function: Determine the version number of the program 248 Example : 249 Returns : float or undef 250 Args : none 251 252=cut 253 254sub version { 255 my ($self) = @_; 256 my $exe; 257 # Kalign version 2.01, Copyright (C) 2004, 2005, 2006 Timo Lassmann 258 return undef unless $exe = $self->executable; 259 my $string = `$exe 2>&1` ; 260 $string =~ /Kalign\s+version\s+(\d+\.\d+)/m; 261 return $1 || undef; 262} 263 264=head2 run 265 266 Title : run 267 Usage : my $output = $application->run(\@seqs); 268 Function: Generic run of an application 269 Returns : Bio::SimpleAlign object 270 Args : Arrayref of Bio::PrimarySeqI objects or 271 a filename to run on 272 273=cut 274 275sub run { 276 my $self = shift; 277 return $self->align(shift); 278} 279 280=head2 align 281 282 Title : align 283 Usage : 284 $inputfilename = 't/data/cysprot.fa'; 285 $aln = $factory->align($inputfilename); 286or 287 $seq_array_ref = \@seq_array; 288 # @seq_array is array of Seq objs 289 $aln = $factory->align($seq_array_ref); 290 Function: Perform a multiple sequence alignment 291 Returns : Reference to a SimpleAlign object containing the 292 sequence alignment. 293 Args : Name of a file containing a set of unaligned fasta sequences 294 or else an array of references to Bio::Seq objects. 295 296 Throws an exception if argument is not either a string (eg a 297 filename) or a reference to an array of Bio::Seq objects. If 298 argument is string, throws exception if file corresponding to string 299 name can not be found. If argument is Bio::Seq array, throws 300 exception if less than two sequence objects are in array. 301 302=cut 303 304sub align { 305 my ($self,$input) = @_; 306 # Create input file pointer 307 $self->io->_io_cleanup(); 308 my $infilename; 309 if( defined $input ) { 310 $infilename = $self->_setinput($input); 311 } elsif( defined $self->in ) { 312 $infilename = $self->_setinput($self->in); 313 } else { 314 $self->throw("No inputdata provided\n"); 315 } 316 if (! $infilename) { 317 $self->throw("Bad input data or less than 2 sequences in $input !"); 318 } 319 320 my $param_string = $self->_setparams(); 321 322 # run kalign 323 return &_run($self, $infilename, $param_string); 324} 325 326=head2 _run 327 328 Title : _run 329 Usage : Internal function, not to be called directly 330 Function: makes actual system call to kalign program 331 Example : 332 Returns : nothing; kalign output is written to a 333 temporary file OR specified output file 334 Args : Name of a file containing a set of unaligned fasta sequences 335 and hash of parameters to be passed to kalign 336 337 338=cut 339 340sub _run { 341 my ($self,$infilename,$params) = @_; 342 my $commandstring = $self->executable." -in $infilename $params"; 343 344 $self->debug( "kalign command = $commandstring \n"); 345 346 my $status = system($commandstring); 347 my $outfile = $self->outfile_name(); 348 if( !-e $outfile || -z $outfile ) { 349 $self->warn( "Kalign call crashed: $? [command $commandstring]\n"); 350 return undef; 351 } 352 353 my $in = Bio::AlignIO->new('-file' => $outfile, 354 '-format' => $self->aformat); 355 my $aln = $in->next_aln(); 356 return $aln; 357} 358 359 360=head2 _setinput 361 362 Title : _setinput 363 Usage : Internal function, not to be called directly 364 Function: Create input file for kalign program 365 Example : 366 Returns : name of file containing kalign data input AND 367 Args : Arrayref of Seqs or input file name 368 369 370=cut 371 372sub _setinput { 373 my ($self,$input) = @_; 374 my ($infilename, $seq, $temp, $tfh); 375 if (! ref $input) { 376 # check that file exists or throw 377 $infilename = $input; 378 unless (-e $input) {return 0;} 379 # let's peek and guess 380 open(IN,$infilename) || $self->throw("Cannot open $infilename"); 381 my $header; 382 while( defined ($header = <IN>) ) { 383 last if $header !~ /^\s+$/; 384 } 385 close(IN); 386 if ( $header !~ /^>\s*\S+/ ){ 387 $self->throw("Need to provide a FASTA format file to kalign!"); 388 } 389 return ($infilename); 390 } elsif (ref($input) =~ /ARRAY/i ) { # $input may be an 391 # array of BioSeq objects... 392 # Open temporary file for both reading & writing of array 393 ($tfh,$infilename) = $self->io->tempfile(); 394 if( ! ref($input->[0]) ) { 395 $self->warn("passed an array ref which did not contain objects to _setinput"); 396 return undef; 397 } elsif( $input->[0]->isa('Bio::PrimarySeqI') ) { 398 $temp = Bio::SeqIO->new('-fh' => $tfh, 399 '-format' => 'fasta'); 400 my $ct = 1; 401 foreach $seq (@$input) { 402 return 0 unless ( ref($seq) && 403 $seq->isa("Bio::PrimarySeqI") ); 404 if( ! defined $seq->display_id || 405 $seq->display_id =~ /^\s+$/) { 406 $seq->display_id( "Seq".$ct++); 407 } 408 $temp->write_seq($seq); 409 } 410 $temp->close(); 411 undef $temp; 412 close($tfh); 413 $tfh = undef; 414 } else { 415 $self->warn( "got an array ref with 1st entry ". 416 $input->[0]. 417 " and don't know what to do with it\n"); 418 } 419 return ($infilename); 420 } else { 421 $self->warn("Got $input and don't know what to do with it\n"); 422 } 423 return 0; 424} 425 426 427=head2 _setparams 428 429 Title : _setparams 430 Usage : Internal function, not to be called directly 431 Function: Create parameter inputs for kalign program 432 Example : 433 Returns : parameter string to be passed to kalign 434 during align or profile_align 435 Args : name of calling object 436 437=cut 438 439sub _setparams { 440 my ($self) = @_; 441 my ($attr, $value,$param_string); 442 $param_string = ''; 443 my $laststr; 444 for $attr ( @KALIGN_PARAMS ) { 445 $value = $self->$attr(); 446 next unless (defined $value); 447 my $attr_key = lc $attr; 448 $attr_key = ' -'.$attr_key; 449 $param_string .= $attr_key .' '.$value; 450 451 } 452 for $attr ( @KALIGN_SWITCHES) { 453 $value = $self->$attr(); 454 next unless ($value); 455 my $attr_key = lc $attr; #put switches in format expected by tcoffee 456 $attr_key = ' -'.$attr_key; 457 $param_string .= $attr_key ; 458 } 459 460 # Set default output file if no explicit output file selected 461 unless ($self->outfile_name ) { 462 my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir()); 463 close($tfh); 464 undef $tfh; 465 $self->outfile_name($outfile); 466 } 467 $param_string .= " -out ".$self->outfile_name; 468 469 if ($self->quiet() || $self->verbose < 0) { 470 my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null'; 471 $param_string .= " 2> $null"; 472 } 473 return $param_string; 474} 475 476=head2 aformat 477 478 Title : aformat 479 Usage : my $alignmentformat = $self->aformat(); 480 Function: Get/Set alignment format 481 Returns : string 482 Args : string 483 484 485=cut 486 487sub aformat{ 488 my $self = shift; 489 $self->{'_aformat'} = shift if @_; 490 return $self->{'_aformat'}; 491} 492 493=head1 Bio::Tools::Run::BaseWrapper methods 494 495=cut 496 497=head2 no_param_checks 498 499 Title : no_param_checks 500 Usage : $obj->no_param_checks($newval) 501 Function: Boolean flag as to whether or not we should 502 trust the sanity checks for parameter values 503 Returns : value of no_param_checks 504 Args : newvalue (optional) 505 506 507=cut 508 509=head2 save_tempfiles 510 511 Title : save_tempfiles 512 Usage : $obj->save_tempfiles($newval) 513 Function: 514 Returns : value of save_tempfiles 515 Args : newvalue (optional) 516 517 518=cut 519 520=head2 outfile_name 521 522 Title : outfile_name 523 Usage : my $outfile = $kalign->outfile_name(); 524 Function: Get/Set the name of the output file for this run 525 (if you wanted to do something special) 526 Returns : string 527 Args : [optional] string to set value to 528 529 530=cut 531 532 533=head2 tempdir 534 535 Title : tempdir 536 Usage : my $tmpdir = $self->tempdir(); 537 Function: Retrieve a temporary directory name (which is created) 538 Returns : string which is the name of the temporary directory 539 Args : none 540 541 542=cut 543 544=head2 cleanup 545 546 Title : cleanup 547 Usage : $kalign->cleanup(); 548 Function: Will cleanup the tempdir directory 549 Returns : none 550 Args : none 551 552 553=cut 554 555=head2 io 556 557 Title : io 558 Usage : $obj->io($newval) 559 Function: Gets a L<Bio::Root::IO> object 560 Returns : L<Bio::Root::IO> 561 Args : none 562 563 564=cut 565 5661; # Needed to keep compiler happy 567