3 # You may distribute this module under the same terms as perl itself
5 # POD documentation - main docs before the code
9 # March 2007 - first full implementation; needs some file IO tweaking between
10 # runs but works for now
11 # April 2008 - add 0.81 parameters (may be removed in the 1.0 release)
13 # July 2009 - updated for v1.0. No longer supporting pre-1.0 Infernal
17 Bio::Tools::Run::Infernal - Wrapper for local execution of cmalign, cmbuild,
22 # parameters which are switches are set with any value that evals TRUE,
23 # others are set to a specific value
25 my $factory = Bio::Tools::Run::Infernal->new(@params);
27 # run cmalign|cmbuild|cmsearch|cmscore|cmemit directly as a wrapper method
28 # this resets the program flag if previously set
30 $factory->cmsearch(@seqs); # searches Bio::PrimarySeqI's based on set cov. model
31 # saves output to optional outfile_name, returns
34 # only values which are allowed for a program are set, so one can use the same
35 # wrapper for the following...
37 $factory->cmalign(@seqs); # aligns Bio::PrimarySeqI's to a set cov. model,
38 # --merge option allows two alignments generated
39 # from the same CM to be merged.
40 # output to outfile_name, returns Bio::AlignIO
41 $factory->cmscore(); # scores set cov. model against Bio::PrimarySeqI,
42 # output to outfile_name/STDOUT.
43 $factory->cmbuild($aln); # builds covariance model based on alignment
44 # CM to outfile_name or model_file (one is required
45 # here), output to STDOUT.
46 $factory->cmemit(); # emits sequence from specified cov. model;
47 # set one if no file specified. output to
48 # outfile_name, returns Bio::SeqIO or (if -a is set)
50 $factory->cmcalibrate($file); # calibrates specified cov. model; output to
52 $factory->cmstat($file); # summary stats for cov. model; set one if no file
53 # specified; output to STDOUT
55 # run based on the setting of the program parameter
57 my $factory = Bio::Tools::Run::Infernal->new(-program => 'cmsearch',
59 my $search = $factory->run($seq);
61 # using cmsearch returns a Bio::SearchIO object
63 while (my $result = $searchio->next_result){
64 while(my $hit = $result->next_hit){
65 while (my $hsp = $hit->next_hsp){
66 print join("\t", ( $r->query_name,
79 Wrapper module for Sean Eddy's Infernal suite of programs. The current
80 implementation runs cmsearch, cmcalibrate, cmalign, cmemit, cmbuild, cmscore,
81 and cmstat. cmsearch will return a Bio::SearchIO, cmemit a Bio::SeqIO/AlignIO,
82 and cmalign a Bio::AlignIO. All others send output to STDOUT. Optionally,
83 any program's output can be redirected to outfile_name.
85 We HIGHLY suggest upgrading to Infernal 1.0. In that spirit, this wrapper now
86 supports parameters for Infernal 1.0 only; for wrapping older versions of
87 Infernal we suggest using the version of Bio::Tools::Run::Infernal that came
88 with previous versions of BioPerl-run.
90 NOTE: Due to conflicts in the way Infernal parameters are now formatted vs.
91 subroutine naming in Perl (specifically the inclusion of hyphens) and due to the
92 very large number of parameters available, setting and resetting parameters via
93 set_parameters() and reset_parameters() is required. All valid parameters can
94 be set, but only ones valid for the executable set via program()/program_name()
95 are used for calling the executables, the others are silently ignored.
101 User feedback is an integral part of the evolution of this and other
102 Bioperl modules. Send your comments and suggestions preferably to one
103 of the Bioperl mailing lists. Your participation is much appreciated.
105 bioperl-l@bioperl.org - General discussion
106 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
110 Please direct usage questions or support issues to the mailing list:
112 I<bioperl-l@bioperl.org>
114 rather than to the module maintainer directly. Many experienced and
115 reponsive experts will be able look at the problem and quickly
116 address it. Please include a thorough description of the problem
117 with code and data examples if at all possible.
119 =head2 Reporting Bugs
121 Report bugs to the Bioperl bug tracking system to help us keep track
122 the bugs and their resolution. Bug reports can be submitted via the
125 http://redmine.open-bio.org/projects/bioperl/
127 =head1 AUTHOR - Chris Fields
129 Email: cjfields-at-uiuc-dot-edu
133 cjfields-at-uiuc-dot-edu
137 The rest of the documentation details each of the object
138 methods. Internal methods are usually preceded with a _
142 package Bio
::Tools
::Run
::Infernal
;
146 use base
qw(Bio::Root::Root Bio::Tools::Run::WrapperBase Bio::ParameterBaseI);
153 # yes, these are the current parameters
154 our %INFERNAL_PARAMS = (
155 'A' => ['switch', '-', qw(cmbuild)],
156 'E' => ['param', '-', qw(cmsearch cmstat)],
157 'F' => ['switch', '-', qw(cmbuild)],
158 'Lmax' => ['param', '--', qw(cmscore)],
159 'Lmin' => ['param', '--', qw(cmscore)],
160 'T' => ['param', '-', qw(cmsearch cmstat)],
161 'Wbeta' => ['param', '--', qw(cmbuild)],
162 'Z' => ['param', '-', qw(cmsearch cmstat)],
163 'a' => ['switch', '-', qw(cmbuild cmemit cmscore)],
164 'afile' => ['param', '--', qw(cmstat)],
165 'ahmm' => ['param', '--', qw(cmemit)],
166 'all' => ['switch', '--', qw(cmstat)],
167 'aln-hbanded' => ['switch', '--', qw(cmsearch)],
168 'aln-optacc' => ['switch', '--', qw(cmsearch)],
169 'aln2bands' => ['switch', '--', qw(cmscore cmsearch)],
170 'banddump' => ['param', '--', qw(cmalign)],
171 'begin' => ['param', '--', qw(cmemit)],
172 'beta' => ['param', '--', qw(cmalign cmscore cmsearch cmstat)],
173 'betae' => ['param', '--', qw(cmscore)],
174 'betas' => ['param', '--', qw(cmscore)],
175 'bfile' => ['param', '--', qw(cmstat)],
176 'binary' => ['switch', '--', qw(cmbuild)],
177 'bits' => ['switch', '--', qw(cmstat)],
178 'bottomonly' => ['switch', '--', qw(cmsearch)],
179 'c' => ['switch', '-', qw(cmemit)],
180 'call' => ['switch', '--', qw(cmbuild)],
181 'cdump' => ['param', '--', qw(cmbuild)],
182 'cfile' => ['param', '--', qw(cmbuild)],
183 'checkfb' => ['switch', '--', qw(cmalign)],
184 'checkpost' => ['switch', '--', qw(cmalign)],
185 'cmL' => ['param', '--', qw(cmstat)],
186 'cmaxid' => ['param', '--', qw(cmbuild)],
187 'cmtbl' => ['param', '--', qw(cmbuild)],
188 'corig' => ['switch', '--', qw(cmbuild)],
189 'ctarget' => ['param', '--', qw(cmbuild)],
190 'cyk' => ['switch', '--', qw(cmalign cmbuild cmsearch)],
191 'devhelp' => ['switch', '--', qw(cmalign cmbuild cmcalibrate cmemit cmscore cmsearch)],
192 'dlev' => ['param', '--', qw(cmalign)],
193 'dna' => ['switch', '--', qw(cmalign cmemit cmsearch)],
194 'eX' => ['param', '--', qw(cmbuild)],
195 'eent' => ['switch', '--', qw(cmbuild)],
196 'efile' => ['param', '--', qw(cmstat)],
197 'ehmmre' => ['param', '--', qw(cmbuild)],
198 'elself' => ['param', '--', qw(cmbuild)],
199 'emap' => ['param', '--', qw(cmbuild)],
200 'emit' => ['switch', '--', qw(cmscore)],
201 'end' => ['param', '--', qw(cmemit)],
202 'enone' => ['switch', '--', qw(cmbuild)],
203 'ere' => ['param', '--', qw(cmbuild)],
204 'exp' => ['param', '--', qw(cmemit)],
205 'exp-T' => ['param', '--', qw(cmcalibrate)],
206 'exp-beta' => ['param', '--', qw(cmcalibrate)],
207 'exp-cmL-glc' => ['param', '--', qw(cmcalibrate)],
208 'exp-cmL-loc' => ['param', '--', qw(cmcalibrate)],
209 'exp-ffile' => ['param', '--', qw(cmcalibrate)],
210 'exp-fract' => ['param', '--', qw(cmcalibrate)],
211 'exp-gc' => ['param', '--', qw(cmcalibrate)],
212 'exp-hfile' => ['param', '--', qw(cmcalibrate)],
213 'exp-hmmLn-glc' => ['param', '--', qw(cmcalibrate)],
214 'exp-hmmLn-loc' => ['param', '--', qw(cmcalibrate)],
215 'exp-hmmLx' => ['param', '--', qw(cmcalibrate)],
216 'exp-no-qdb' => ['switch', '--', qw(cmcalibrate)],
217 'exp-pfile' => ['param', '--', qw(cmcalibrate)],
218 'exp-qqfile' => ['param', '--', qw(cmcalibrate)],
219 'exp-random' => ['switch', '--', qw(cmcalibrate)],
220 'exp-sfile' => ['param', '--', qw(cmcalibrate)],
221 'exp-tailn-cglc' => ['param', '--', qw(cmcalibrate)],
222 'exp-tailn-cloc' => ['param', '--', qw(cmcalibrate)],
223 'exp-tailn-hglc' => ['param', '--', qw(cmcalibrate)],
224 'exp-tailn-hloc' => ['param', '--', qw(cmcalibrate)],
225 'exp-tailp' => ['param', '--', qw(cmcalibrate)],
226 'exp-tailxn' => ['param', '--', qw(cmcalibrate)],
227 'fil-E-hmm' => ['param', '--', qw(cmsearch)],
228 'fil-E-qdb' => ['param', '--', qw(cmsearch)],
229 'fil-F' => ['param', '--', qw(cmcalibrate)],
230 'fil-N' => ['param', '--', qw(cmcalibrate)],
231 'fil-Smax-hmm' => ['param', '--', qw(cmsearch)],
232 'fil-T-hmm' => ['param', '--', qw(cmsearch)],
233 'fil-T-qdb' => ['param', '--', qw(cmsearch)],
234 'fil-aln2bands' => ['switch', '--', qw(cmcalibrate)],
235 'fil-beta' => ['param', '--', qw(cmsearch)],
236 'fil-dfile' => ['param', '--', qw(cmcalibrate)],
237 'fil-gemit' => ['switch', '--', qw(cmcalibrate)],
238 'fil-no-hmm' => ['switch', '--', qw(cmsearch)],
239 'fil-no-qdb' => ['switch', '--', qw(cmsearch)],
240 'fil-nonbanded' => ['switch', '--', qw(cmcalibrate)],
241 'fil-tau' => ['param', '--', qw(cmcalibrate)],
242 'fil-xhmm' => ['param', '--', qw(cmcalibrate)],
243 'fins' => ['switch', '--', qw(cmalign cmbuild)],
244 'forecast' => ['param', '--', qw(cmcalibrate cmsearch)],
245 'forward' => ['switch', '--', qw(cmscore cmsearch)],
246 'g' => ['switch', '-', qw(cmsearch cmstat)],
247 'ga' => ['switch', '--', qw(cmsearch cmstat)],
248 'gapthresh' => ['param', '--', qw(cmalign cmbuild)],
249 'gcfile' => ['param', '--', qw(cmsearch)],
250 'ge' => ['switch', '--', qw(cmstat)],
251 'gfc' => ['switch', '--', qw(cmstat)],
252 'gfi' => ['switch', '--', qw(cmstat)],
253 'gibbs' => ['switch', '--', qw(cmbuild)],
254 'gtbl' => ['param', '--', qw(cmbuild)],
255 'gtree' => ['param', '--', qw(cmbuild)],
256 'h' => ['switch', '-', qw(cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat)],
257 'hbanded' => ['switch', '--', qw(cmalign cmscore cmsearch)],
258 'hmm-W' => ['param', '--', qw(cmsearch)],
259 'hmm-cW' => ['param', '--', qw(cmsearch)],
260 'hmmL' => ['param', '--', qw(cmstat)],
261 'hsafe' => ['switch', '--', qw(cmalign cmscore)],
262 'ignorant' => ['switch', '--', qw(cmbuild)],
263 'iins' => ['switch', '--', qw(cmbuild)],
264 'infile' => ['param', '--', qw(cmscore)],
265 'informat' => ['param', '--', qw(cmalign cmbuild cmsearch)],
266 'inside' => ['switch', '--', qw(cmalign cmscore cmsearch)],
267 'l' => ['switch', '-', qw(cmalign cmbuild cmemit cmscore)],
268 'lambda' => ['param', '--', qw(cmsearch)],
269 'le' => ['switch', '--', qw(cmstat)],
270 'lfc' => ['switch', '--', qw(cmstat)],
271 'lfi' => ['switch', '--', qw(cmstat)],
272 'm' => ['switch', '-', qw(cmstat)],
273 'matchonly' => ['switch', '--', qw(cmalign)],
274 'merge' => ['switch', '--', qw(cmalign)],
275 'mpi' => ['switch', '--', qw(cmalign cmcalibrate cmscore cmsearch)],
276 'mxsize' => ['param', '--', qw(cmalign cmbuild cmcalibrate cmscore cmsearch)],
277 'n' => ['param', '-', qw(cmbuild cmemit cmscore)],
278 'nc' => ['switch', '--', qw(cmsearch cmstat)],
279 'no-null3' => ['switch', '--', qw(cmalign cmcalibrate cmscore cmsearch)],
280 'no-qdb' => ['switch', '--', qw(cmsearch)],
281 'noalign' => ['switch', '--', qw(cmsearch)],
282 'nobalance' => ['switch', '--', qw(cmbuild)],
283 'nodetach' => ['switch', '--', qw(cmbuild)],
284 'nonbanded' => ['switch', '--', qw(cmalign cmbuild cmscore)],
285 'null' => ['param', '--', qw(cmbuild)],
286 'null2' => ['switch', '--', qw(cmsearch)],
287 'o' => ['param', '-', qw(cmalign cmsearch)],
288 'old' => ['switch', '--', qw(cmscore)],
289 'onepost' => ['switch', '--', qw(cmalign)],
290 'optacc' => ['switch', '--', qw(cmalign)],
291 'outfile' => ['param', '--', qw(cmscore)],
292 'p' => ['switch', '-', qw(cmalign cmsearch)],
293 'pad' => ['switch', '--', qw(cmscore)],
294 'pbegin' => ['param', '--', qw(cmalign cmcalibrate cmemit cmscore cmsearch)],
295 'pbswitch' => ['param', '--', qw(cmbuild)],
296 'pebegin' => ['switch', '--', qw(cmalign cmcalibrate cmemit cmscore cmsearch)],
297 'pend' => ['param', '--', qw(cmalign cmcalibrate cmemit cmscore cmsearch)],
298 'pfend' => ['param', '--', qw(cmalign cmcalibrate cmemit cmscore cmsearch)],
299 'prior' => ['param', '--', qw(cmbuild)],
300 'q' => ['switch', '-', qw(cmalign)],
301 'qdb' => ['switch', '--', qw(cmalign cmscore)],
302 'qdbboth' => ['switch', '--', qw(cmscore)],
303 'qdbfile' => ['param', '--', qw(cmstat)],
304 'qdbsmall' => ['switch', '--', qw(cmscore)],
305 'random' => ['switch', '--', qw(cmscore)],
306 'rdump' => ['param', '--', qw(cmbuild)],
307 'refine' => ['param', '--', qw(cmbuild)],
308 'regress' => ['param', '--', qw(cmalign cmbuild cmscore)],
309 'resonly' => ['switch', '--', qw(cmalign)],
310 'rf' => ['switch', '--', qw(cmalign cmbuild)],
311 'rna' => ['switch', '--', qw(cmalign cmemit cmsearch)],
312 'rsearch' => ['param', '--', qw(cmbuild)],
313 'rtrans' => ['switch', '--', qw(cmsearch)],
314 's' => ['param', '-', qw(cmalign cmbuild cmcalibrate cmemit cmscore)],
315 'sample' => ['switch', '--', qw(cmalign)],
316 'scoreonly' => ['switch', '--', qw(cmscore)],
317 'search' => ['switch', '--', qw(cmscore cmstat)],
318 'seqfile' => ['param', '--', qw(cmstat)],
319 'sfile' => ['param', '--', qw(cmstat)],
320 'shmm' => ['param', '--', qw(cmemit)],
321 'small' => ['switch', '--', qw(cmalign)],
322 'stall' => ['switch', '--', qw(cmalign cmscore cmsearch)],
323 'sub' => ['switch', '--', qw(cmalign cmbuild cmscore)],
324 'sums' => ['switch', '--', qw(cmalign cmsearch)],
325 'tabfile' => ['param', '--', qw(cmsearch)],
326 'tau' => ['param', '--', qw(cmalign cmbuild cmscore cmsearch)],
327 'taue' => ['param', '--', qw(cmscore)],
328 'taus' => ['param', '--', qw(cmscore)],
329 'tc' => ['switch', '--', qw(cmsearch cmstat)],
330 'tfile' => ['param', '--', qw(cmalign cmbuild cmemit cmscore)],
331 'toponly' => ['switch', '--', qw(cmsearch cmstat)],
332 'u' => ['switch', '-', qw(cmemit)],
333 'v' => ['switch', '-', qw(cmbuild cmcalibrate)],
334 'viterbi' => ['switch', '--', qw(cmalign cmscore cmsearch)],
335 'wblosum' => ['switch', '--', qw(cmbuild)],
336 'wgiven' => ['switch', '--', qw(cmbuild)],
337 'wgsc' => ['switch', '--', qw(cmbuild)],
338 'wid' => ['param', '--', qw(cmbuild)],
339 'withali' => ['param', '--', qw(cmalign)],
340 'withpknots' => ['switch', '--', qw(cmalign)],
341 'wnone' => ['switch', '--', qw(cmbuild)],
342 'wpb' => ['switch', '--', qw(cmbuild)],
343 'x' => ['switch', '-', qw(cmsearch)],
344 'xfile' => ['param', '--', qw(cmstat)],
347 our %INFERNAL_PROGRAM = (
348 'cmalign' => "cmalign [-options] <cmfile> <sequence file>\n".
349 'cmalign [-options] --merge <cmfile> <msafile1> <msafile2>',
350 'cmbuild' => 'cmbuild [-options] <cmfile output> <alignment file>',
351 'cmcalibrate' => 'cmcalibrate [-options] <cmfile>',
352 'cmemit' => 'cmemit [-options] <cmfile> <sequence output file>',
353 'cmscore' => 'cmscore [-options] <cmfile>',
354 'cmsearch' => 'cmsearch [-options] <cmfile> <sequence file>',
355 'cmstat' => 'cmstat [-options] <cmfile>',
358 # this is a simple lookup for easy validation for passed methods
359 our %LOCAL_PARAMS = map {$_ => 1} qw(program outfile tempfile model);
364 Usage : my $wrapper = Bio::Tools::Run::Infernal->new(@params)
365 Function: creates a new Infernal factory
366 Returns: Bio::Tools::Run::Infernal wrapper
367 Args : list of parameters
372 my ($class,@args) = @_;
373 my $self = $class->SUPER::new
(@args);
375 # these are specific parameters we do not want passed on to set_parameters
376 my ($program, $model, $validate, $q, $o1, $o2) =
377 $self->_rearrange([qw(PROGRAM
385 $self->warn("Only assign to either -outfile_name or -o, not both;");
387 my $out = $o1 || $o2;
388 $self->validate_parameters($validate);
389 $q && $self->quiet($q);
390 $program && $self->program($program);
391 $model && $self->model_file($model);
393 $self->outfile_name($out);
394 $self->io->_initialize_io();
395 $self->set_parameters(@args);
402 Usage : $obj->program()
403 Function: Set the program called when run() is used. Synonym of
405 Returns : String (program name)
406 Args : String (program name)
407 Status : Unstable (may delegate to program_name, which is the interface method)
413 return $self->program_name(@_);
419 Usage : $factory>program_name()
420 Function: holds the program name
430 $self->throw("Program '$p' not supported")
431 if !exists $INFERNAL_PROGRAM{lc $p};
432 $self->{'_program'} = lc $p;
433 # set up cache of valid parameters
434 while (my ($p, $data) = each %INFERNAL_PARAMS) {
435 my %in_exe = map {$_ => 1} @
$data[2..$#{$data}];
436 $self->{valid_params
}->{$p} = 1 if exists $in_exe{$self->{'_program'}};
439 return $self->{'_program'};
445 Usage : $obj->model_file()
446 Function: Set the model file used when run() is called.
447 Returns : String (file location of covariance model)
448 Args : String (file location of covariance model)
454 return $self->{'_model_file'} = shift if @_;
455 return $self->{'_model_file'};
461 Usage : $factory->program_dir(@params)
462 Function: returns the program directory, obtained from ENV variable.
469 my ($self, $dir) = @_;
471 $self->{_program_dir
} = $dir;
473 return Bio
::Root
::IO
->catfile($ENV{INFERNALDIR
}) || '';
479 Usage : $v = $prog->version();
480 Function: Determine the version number of the program (uses cmsearch)
482 Returns : float or undef
489 return unless $self->executable;
490 my $exe = $self->executable;
491 my $string = `$exe -h 2>&1`;
493 if ($string =~ m{Infernal\s([\d.]+)}) {
495 $self->deprecated(-message
=> "Only Infernal 1.0 and above is supported.",
496 -version
=> 1.006001) if $v < 1;
498 return $self->{'_progversion'} = $v || undef;
504 Usage : $obj->run($seqFile)
505 Function: Runs Infernal and returns Bio::SearchIO
506 Returns : A Bio::SearchIO
507 Args : A Bio::PrimarySeqI or file name
511 # TODO: update to accept multiple seqs, alignments
513 my ($self,@seq) = @_;
514 if (ref $seq[0] && $seq[0]->isa("Bio::PrimarySeqI") ){# it is an object
515 my $infile1 = $self->_writeSeqFile(@seq);
516 return $self->_run($infile1);
517 } elsif (ref $seq[0] && $seq[0]->isa("Bio::Align::AlignI") ){ # it is an object
518 my $infile1 = $self->_writeAlignFile(@seq);
519 return $self->_run($infile1);
521 return $self->_run(@seq);
525 =head1 Specific program interface methods
530 Usage : $obj->cmsearch($seqFile)
531 Function: Runs Infernal cmsearch and returns Bio::SearchIO
532 Returns : A Bio::SearchIO
533 Args : Bio::PrimarySeqI or file name
538 my ($self,@seq) = @_;
539 $self->program('cmsearch');
540 if (ref $seq[0] && $seq[0]->isa("Bio::PrimarySeqI") ){# it is an object
541 my $infile1 = $self->_writeSeqFile(@seq);
542 return $self->_run(-seq_files
=> [$infile1]);
544 return $self->_run(-seq_files
=> \
@seq);
551 Usage : $obj->cmalign($seqFile)
552 Function: Runs Infernal cmalign and returns Bio::AlignIO
553 Returns : A Bio::AlignIO
554 Args : Bio::PrimarySeqI or file name
559 my ($self,@seq) = @_;
560 $self->program('cmalign');
561 if (ref $seq[0]) { # it is an object
562 if ($seq[0]->isa("Bio::PrimarySeqI") ){
563 my $infile1 = $self->_writeSeqFile(@seq);
564 return $self->_run(-seq_files
=> [$infile1]);
565 } elsif ( $seq[0]->isa("Bio::Align::AlignI") ) {
566 if (scalar(@seq) != 2) {
569 my $infile1 = $self->_writeAlignFile($seq[0]);
570 my $infile2 = $self->_writeAlignFile($seq[1]);
571 return $self->_run(-align_files
=> [$infile1, $infile2]);
574 # we can maybe add a check for the file extension and try to DTRT
575 my %params = $self->get_parameters('valid');
576 $params{merge
} ?
return $self->_run(-align_files
=> \
@seq):
577 return $self->_run(-seq_files
=> \
@seq);
578 return $self->_run(-seq_files
=> \
@seq);
585 Usage : $obj->cmemit($modelfile)
586 Function: Runs Infernal cmemit and returns Bio::AlignIO
587 Returns : A Bio::AlignIO
588 Args : None; set model_file() to use a specific model
594 $self->program('cmemit');
595 return $self->_run(@_);
601 Usage : $obj->cmbuild($alignment)
602 Function: Runs Infernal cmbuild and saves covariance model
603 Returns : 1 on success (no object for covariance models)
604 Args : Bio::AlignIO with structural information (such as from Stockholm
605 format source) or alignment file name
610 my ($self,@seq) = @_;
611 $self->program('cmbuild');
612 if (ref $seq[0] && $seq[0]->isa("Bio::Align::AlignI") ){# it is an object
613 my $infile1 = $self->_writeAlignFile(@seq);
614 return $self->_run(-align_files
=> [$infile1]);
616 return $self->_run(-align_files
=> \
@seq);
623 Usage : $obj->cmscore($seq)
624 Function: Runs Infernal cmscore and saves output
626 Args : None; set model_file() to use a specific model
631 my ($self,@seq) = @_;
632 $self->program('cmscore');
633 return $self->_run();
639 Usage : $obj->cmcalibrate('file')
640 Function: Runs Infernal calibrate on specified CM
642 Args : None; set model_file() to use a specific model
647 my ($self,@seq) = @_;
648 $self->program('cmcalibrate');
649 return $self->_run();
655 Usage : $obj->cmstat($seq)
656 Function: Runs Infernal cmstat and saves output
658 Args : None; set model_file() to use a specific model
663 my ($self,@seq) = @_;
664 $self->program('cmstat');
665 return $self->_run();
668 =head1 Bio::ParameterBaseI-specific methods
670 These methods are part of the Bio::ParameterBaseI interface
674 =head2 set_parameters
676 Title : set_parameters
677 Usage : $pobj->set_parameters(%params);
678 Function: sets the parameters listed in the hash or array
680 Args : [optional] hash or array of parameter/values. These can optionally
681 be hash or array references
682 Note : This only sets parameters; to set methods use the method name
687 # circumvent any issues arising from passing in refs
688 my %args = (ref($_[0]) eq 'HASH') ?
%{$_[0]} :
689 (ref($_[0]) eq 'ARRAY') ? @
{$_[0]} :
691 # set the parameters passed in, but only ones supported for the program
692 my ($prog, $validate) = ($self->program, $self->validate_parameters);
695 %args = map { my $a = $_;
700 while (my ($key, $val) = each %args) {
701 if (exists $INFERNAL_PARAMS{$key}) {
702 my ($type, $prefix) = @
{$INFERNAL_PARAMS{$key}}[0..1];
703 @
{$self->{parameters
}->{$key}} = ($type, $prefix);
704 unshift @
{$self->{parameters
}->{$key}},
705 $type eq 'param' ?
$val :
706 $type eq 'switch' && $val ?
1 : 0;
708 my %in_exe = map {$_ => 1} @
{$INFERNAL_PARAMS{$key}}[2..$#{$INFERNAL_PARAMS{$key}}];
709 $self->warn("Parameter $key not used for $prog") if !exists $in_exe{$key};
712 $self->warn("Parameter $key does not exist") if ($validate);
717 =head2 reset_parameters
719 Title : reset_parameters
720 Usage : resets values
721 Function: resets parameters to either undef or value in passed hash
723 Args : [optional] hash of parameter-value pairs
727 sub reset_parameters
{
729 delete $self->{parameters
};
731 $self->set_parameters(@_);
735 =head2 validate_parameters
737 Title : validate_parameters
738 Usage : $pobj->validate_parameters(1);
739 Function: sets a flag indicating whether to validate parameters via
740 set_parameters() or reset_parameters()
742 Args : [optional] value evaluating to True/False
743 Note : Optionally implemented method; up to the implementation on whether
744 to automatically validate parameters or optionally do so
748 sub validate_parameters
{
751 $self->{validate_params
} = defined $_[0] ?
1 : 0;
753 return $self->{validate_params
};
756 =head2 parameters_changed
758 Title : parameters_changed
759 Usage : if ($pobj->parameters_changed) {...}
760 Function: Returns boolean true (1) if parameters have changed
761 Returns : Boolean (0 or 1)
763 Note : This module does not run state checks, so this always returns True
767 sub parameters_changed
{ 1 }
769 =head2 available_parameters
771 Title : available_parameters
772 Usage : @params = $pobj->available_parameters()
773 Function: Returns a list of the available parameters
774 Returns : Array of parameters
775 Args : [optional] name of executable being used; defaults to returning all
780 sub available_parameters
{
781 my ($self, $exec) = @_;
784 $self->throw("$exec is not part of the Infernal package") if !exists($INFERNAL_PROGRAM{$exec});
785 for my $p (sort keys %INFERNAL_PARAMS) {
786 if (grep { $exec eq $_ }
787 @
{$INFERNAL_PARAMS{$p}}[2..$#{$INFERNAL_PARAMS{$p}}])
793 @params = (sort keys %INFERNAL_PARAMS, sort keys %LOCAL_PARAMS);
798 =head2 get_parameters
800 Title : get_parameters
801 Usage : %params = $pobj->get_parameters;
802 Function: Returns list of set key-value pairs, parameter => value
803 Returns : List of key-value pairs
805 'full' - this option returns everything associated with the parameter
806 as an array ref value; that is, not just the value but also
807 the value, type, and prefix. Default is value only.
808 'valid'- same a 'full', but only returns the grouping valid for the
809 currently set executable
814 my ($self, $option) = @_;
815 $option ||= ''; # no option
817 if (exists $self->{parameters
}) {
818 %params = (ref $option eq 'ARRAY') ?
(
819 map {$_ => $self->{parameters
}{$_}[0]}
820 grep { exists $self->{parameters
}{$_} } @
$option) :
821 (lc $option eq 'full') ?
822 (%{$self->{parameters
}}) :
823 (lc $option eq 'valid') ?
824 (map {$_ => $self->{parameters
}{$_}}
825 grep { exists $self->{valid_params
}->{$_} } keys %{$self->{parameters
}}) :
826 (map {$_ => $self->{parameters
}{$_}[0]} keys %{$self->{parameters
}});
835 All to_* methods are implementation-specific
841 Title : to_exe_string
842 Usage : $string = $pobj->to_exe_string;
843 Function: Returns string (command line string in this case)
850 my ($self, @passed) = @_;
851 my ($seqs, $aligns) = $self->_rearrange([qw(SEQ_FILES ALIGN_FILES)], @passed);
852 if ($seqs || $aligns) {
853 $self->throw("Seqs or alignments must be an array reference") unless
854 ($seqs && ref($seqs) eq 'ARRAY') || ($aligns && ref($aligns) eq 'ARRAY' );
857 my %args = map {$_ => []} qw(switch param input redirect);
858 my %params = $self->get_parameters('valid');
860 my ($exe, $prog, $model, $outfile) = ($self->executable,
863 $self->outfile_name);
865 $self->throw("Executable not found") unless defined($exe);
867 delete $params{o
} if exists $params{o
};
869 if (!defined($model) && $prog ne 'cmbuild') {
870 $self->throw("model_file() not defined")
875 for my $p (sort keys %params) {
876 if ($params{$p}[0]) {
877 my $val = $params{$p}[1] eq 'param' ?
' '.$params{$p}[0] : '';
878 push @
{$args{$params{$p}[1]}}, $params{$p}[2].$p.$val;
882 # TODO: not sure what happens when we pass in multiple seq or alignment
883 # filenames, may need checking
884 if ($prog eq 'cmscore' || $prog eq 'cmstat' || $prog eq 'cmcalibrate') {
885 push @
{$args{'redirect'}}, "> $outfile" if $outfile;
886 push @
{$args{'input'}}, $model;
887 } elsif ($prog eq 'cmsearch') {
888 if (!defined $seqs) {
889 $self->throw('cmsearch requires a sequence file name');
891 push @
{$args{'param'}}, "-o $outfile" if $outfile;
892 push @
{$args{'input'}}, ($model, @
$seqs);
893 } elsif ($prog eq 'cmalign') {
894 if ($params{'merge'}) {
895 $self->throw('cmalign with --merge option requires two alignment files') if
896 !defined($aligns) || @
$aligns < 2;
897 push @
{$args{'input'}}, ($model, @
$aligns);
899 $self->throw('cmalign requires a sequence file') if
901 push @
{$args{'input'}}, ($model, @
$seqs);
903 push @
{$args{'param'}}, "-o $outfile" if $outfile;
904 } elsif ($prog eq 'cmbuild') {
905 $self->throw('cmbuild requires one alignment file') if
908 push @
{$args{'input'}}, ($model, @
$aligns);
909 push @
{$args{'redirect'}}, "> $outfile" if $outfile;
911 push @
{$args{'input'}}, ($outfile, @
$aligns);
913 } elsif ($prog eq 'cmemit') {
915 $self->throw('cmemit requires an outfile_name; tempfile support not implemented yet');
917 push @
{$args{'input'}}, ($model, ,$outfile);
922 if ($self->quiet && $prog ne 'cmsearch') {
923 if ($prog eq 'cmalign') {
924 push @
{$args{switch
}}, '-q' if !exists $params{q
};
926 push @
{$args{redirect
}}, '> /dev/null';
930 my $string = "$exe ".join(' ',(@
{$args{switch
}},
933 @
{$args{redirect
}}));
938 ############### PRIVATE ###############
943 # Usage : $obj->_run()
944 # Function: Internal(not to be used directly)
951 my %ALLOWED = map {$_ => 1} qw(run cmsearch cmalign cmemit cmbuild
952 cmcalibrate cmstat cmscore);
957 my ($prog, $model, $out, $version) = ($self->program,
962 if (my $caller = (caller(1))[3]) {
963 $caller =~ s{.*::(\w+)$}{$1};
964 $self->throw("Calling _run() from disallowed method") unless exists $ALLOWED{$caller};
966 $self->throw("Can't call _run directly");
969 # a model and a file must be defined for all but cmemit; cmemit must have a
970 # file or model defined (using $file if both are defined)
972 # relevant files are passed on to the string builder
973 my $str = $self->to_exe_string(@_);
974 $self->debug("Infernal command: $str\n");
976 my %has = $self->get_parameters('valid');
979 ($prog eq 'cmsearch') ? Bio
::SearchIO
->new(-format
=> 'infernal',
980 -version
=> $version,
982 ($prog eq 'cmalign' ) ? Bio
::AlignIO
->new(-format
=> 'stockholm') :
983 ($prog eq 'cmemit' && $has{a
}) ? Bio
::AlignIO
->new(-format
=> 'stockholm') :
984 ($prog eq 'cmemit') ? Bio
::SeqIO
->new(-format
=> 'fasta') :
989 my $status = system($str);
990 if($status || !-e
$out || -z
$out ) {
991 my $error = ($!) ?
"$! Status: $status" : "Status: $status";
992 $self->throw( "Infernal call crashed: $error \n[command $str]\n");
995 if ($obj && ref($obj)) {
997 @args = (-file
=> $out);
999 # fh-based (no outfile)
1001 open(my $fh,"$str |") || $self->throw("Infernal call ($str) crashed: $?\n");
1002 if ($obj && ref($obj)) {
1004 @args = (-fh
=> $fh);
1008 while(<$fh>) {$io .= $_;}
1010 $self->debug($io) if $io;
1014 $obj->_initialize_io(@args) if $obj && ref($obj);
1020 =head2 _writeSeqFile
1022 Title : _writeSeqFile
1023 Usage : obj->_writeSeqFile($seq)
1024 Function: Internal(not to be used directly)
1031 my ($self,@seq) = @_;
1032 my ($tfh,$inputfile) = $self->io->tempfile(-dir
=>$self->tempdir);
1033 my $in = Bio
::SeqIO
->new(-fh
=> $tfh , '-format' => 'Fasta');
1034 foreach my $s(@seq){
1044 =head2 _writeAlignFile
1046 Title : _writeAlignFile
1047 Usage : obj->_writeAlignFile($seq)
1048 Function: Internal(not to be used directly)
1054 sub _writeAlignFile
{
1055 my ($self,@align) = @_;
1056 my ($tfh,$inputfile) = $self->io->tempfile(-dir
=>$self->tempdir);
1057 my $in = Bio
::AlignIO
->new('-fh' => $tfh ,
1058 '-format' => 'stockholm');
1059 foreach my $s(@align){
1069 # this is a private sub used to regenerate the class data structures,
1072 # could probably add in a description field if needed...
1077 for my $exec (qw(cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat)) {
1078 my $output = `$exec --devhelp`;
1080 $output = `$exec -h`;
1082 my @lines = split("\n",$output);
1084 for my $line (@lines) {
1085 next if $line =~ /^#/;
1086 if ($line =~ /^\s*(-{1,2})(\S+)\s+(<\S+>)?/) {
1088 ($data{prefix
}, my $p, $data{arg
}) = ($1, $2, $3 ?
'param' : 'switch');
1089 if (exists $params{$p}) {
1090 if ($data{prefix
} ne $params{$p}{prefix
}) {
1091 warn("$data{prefix} for $p in $exec doesn't match prefix for same parameter in ".$params{$p}{exec}[-1].":".$params{$p}{prefix
});
1093 if ($data{arg
} ne $params{$p}{arg
}) {
1094 warn("$data{arg} for $p in $exec doesn't match arg for same parameter in ".$params{$p}{exec}[-1].":".$params{$p}{arg
});
1098 while (my ($key, $val) = each %data) {
1099 $params{$p}->{$key} = $val;
1101 push @
{$params{$p}->{exec}}, $exec;
1102 } elsif ($line =~ /Usage:\s*(.+)$/) {
1103 push @
{$usage{$exec}}, $1;
1110 # generate data structure
1111 print "our %INFERNAL_PARAMS = (\n";
1112 for my $k (sort keys %params) {
1113 printf(" %-17s => [","'$k'");
1114 for my $sub (qw(arg prefix exec)) {
1115 my $str = (ref($params{$k}{$sub}) eq 'ARRAY') ?
1116 "qw(".join(' ', @
{$params{$k}{$sub}}).")" :
1117 "'".$params{$k}{$sub}."',";
1118 printf("%-10s", $str);
1124 # generate usage data structure
1125 print "our %INFERNAL_PROGRAM = (\n";
1126 for my $k (sort keys %usage) {
1127 printf(" %-17s => [\n","'$k'");
1128 print ' '.join(",\n ", map {"'$_'"} @
{$usage{$k}})."\n";