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4f47994 Move Pise modules over to bioperl-pise
cjfields authored
1 # $Id$
2 # BioPerl module for Bio::Tools::Run::PiseApplication::polydot
3 #
4 # Cared for by Catherine Letondal <letondal@pasteur.fr>
5 #
6 # For copyright and disclaimer see below.
7 #
8 # POD documentation - main docs before the code
9
10 =head1 NAME
11
12 Bio::Tools::Run::PiseApplication::polydot
13
14 =head1 SYNOPSIS
15
16 #
17
18 =head1 DESCRIPTION
19
20 Bio::Tools::Run::PiseApplication::polydot
21
22 Bioperl class for:
23
24 POLYDOT Displays all-against-all dotplots of a set of sequences (EMBOSS)
25
26
27 Parameters:
28
29 (see also:
30 http://bioweb.pasteur.fr/seqanal/interfaces/polydot.html
31 for available values):
32
33
34 polydot (String)
35
36 init (String)
37
38 sequences (Sequence)
39 Sequences file to be read in (-sequences)
40 pipe: seqsfile
41
42 wordsize (Integer)
43 Word size (-wordsize)
44
45 data (Switch)
46 Display as data (-data)
47
48 graph (Excl)
49 graph [device to be displayed on] (-graph)
50
51 outfile (OutFile)
52 outfile (-outfile)
53
54 gap (Integer)
55 Gap (in residues) between dotplots (-gap)
56
57 boxit (Switch)
58 Draw a box around each dotplot (-boxit)
59
60 dumpfeat (Switch)
61 Dump all matches as feature files (-dumpfeat)
62
63 format (String)
64 format to Dump out as (-format)
65
66 ext (String)
67 Extension for feature file (-ext)
68
69 auto (String)
70
71 psouput (String)
72
73 =head1 FEEDBACK
74
75 =head2 Mailing Lists
76
77 User feedback is an integral part of the evolution of this and other
78 Bioperl modules. Send your comments and suggestions preferably to
79 the Bioperl mailing list. Your participation is much appreciated.
80
81 bioperl-l@bioperl.org - General discussion
82 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
83
84 =head2 Reporting Bugs
85
86 Report bugs to the Bioperl bug tracking system to help us keep track
87 of the bugs and their resolution. Bug reports can be submitted via the
88 web:
89
90 http://bugzilla.open-bio.org/
91
92 =head1 AUTHOR
93
94 Catherine Letondal (letondal@pasteur.fr)
95
96 =head1 COPYRIGHT
97
98 Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
99 All Rights Reserved.
100
101 This module is free software; you can redistribute it and/or modify
102 it under the same terms as Perl itself.
103
104 =head1 DISCLAIMER
105
106 This software is provided "as is" without warranty of any kind.
107
108 =head1 SEE ALSO
109
110 =over
111
112 =item *
113
114 http://bioweb.pasteur.fr/seqanal/interfaces/polydot.html
115
116 =item *
117
118 Bio::Tools::Run::PiseApplication
119
120 =item *
121
122 Bio::Tools::Run::AnalysisFactory::Pise
123
124 =item *
125
126 Bio::Tools::Run::PiseJob
127
128 =back
129
130 =cut
131
132 #'
133 package Bio::Tools::Run::PiseApplication::polydot;
134
135 use vars qw(@ISA);
136 use strict;
137 use Bio::Tools::Run::PiseApplication;
138
139 @ISA = qw(Bio::Tools::Run::PiseApplication);
140
141 =head2 new
142
143 Title : new()
144 Usage : my $polydot = Bio::Tools::Run::PiseApplication::polydot->new($location, $email, @params);
145 Function: Creates a Bio::Tools::Run::PiseApplication::polydot object.
146 This method should not be used directly, but rather by
147 a Bio::Tools::Run::AnalysisFactory::Pise instance.
148 my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
149 my $polydot = $factory->program('polydot');
150 Example : -
151 Returns : An instance of Bio::Tools::Run::PiseApplication::polydot.
152
153 =cut
154
155 sub new {
156 my ($class, $location, $email, @params) = @_;
157 my $self = $class->SUPER::new($location, $email);
158
159 # -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/polydot.pm
160
161 $self->{COMMAND} = "polydot";
162 $self->{VERSION} = "5.a";
163 $self->{TITLE} = "POLYDOT";
164
165 $self->{DESCRIPTION} = "Displays all-against-all dotplots of a set of sequences (EMBOSS)";
166
167 $self->{OPT_EMAIL} = 0;
168
169 $self->{CATEGORIES} = [
170
171 "alignment:dot plots",
172 ];
173
174 $self->{DOCLINK} = "http://www.uk.embnet.org/Software/EMBOSS/Apps/polydot.html";
175
176 $self->{_INTERFACE_STANDOUT} = undef;
177 $self->{_STANDOUT_FILE} = undef;
178
179 $self->{TOP_PARAMETERS} = [
180 "polydot",
181 "init",
182 "input",
183 "required",
184 "output",
185 "gap",
186 "boxit",
187 "dumpfeat",
188 "format",
189 "ext",
190 "auto",
191 "psouput",
192 "psresults",
193 "metaresults",
194 "dataresults",
195 "pngresults",
196
197 ];
198
199 $self->{PARAMETERS_ORDER} = [
200 "polydot",
201 "init",
202 "input", # input Section
203 "sequences", # Sequences file to be read in (-sequences)
204 "required", # required Section
205 "wordsize", # Word size (-wordsize)
206 "output", # output Section
207 "datasection", # data Section
208 "data", # Display as data (-data)
209 "graph", # graph [device to be displayed on] (-graph)
210 "outfile", # outfile (-outfile)
211 "gap", # Gap (in residues) between dotplots (-gap)
212 "boxit", # Draw a box around each dotplot (-boxit)
213 "dumpfeat", # Dump all matches as feature files (-dumpfeat)
214 "format", # format to Dump out as (-format)
215 "ext", # Extension for feature file (-ext)
216 "auto",
217 "psouput",
218 "psresults",
219 "metaresults",
220 "dataresults",
221 "pngresults",
222
223 ];
224
225 $self->{TYPE} = {
226 "polydot" => 'String',
227 "init" => 'String',
228 "input" => 'Paragraph',
229 "sequences" => 'Sequence',
230 "required" => 'Paragraph',
231 "wordsize" => 'Integer',
232 "output" => 'Paragraph',
233 "datasection" => 'Paragraph',
234 "data" => 'Switch',
235 "graph" => 'Excl',
236 "outfile" => 'OutFile',
237 "gap" => 'Integer',
238 "boxit" => 'Switch',
239 "dumpfeat" => 'Switch',
240 "format" => 'String',
241 "ext" => 'String',
242 "auto" => 'String',
243 "psouput" => 'String',
244 "psresults" => 'Results',
245 "metaresults" => 'Results',
246 "dataresults" => 'Results',
247 "pngresults" => 'Results',
248
249 };
250
251 $self->{FORMAT} = {
252 "init" => {
253 "perl" => ' "" ',
254 },
255 "input" => {
256 },
257 "sequences" => {
258 "perl" => '" -sequences=$value -sformat=fasta"',
259 },
260 "required" => {
261 },
262 "wordsize" => {
263 "perl" => '" -wordsize=$value"',
264 },
265 "output" => {
266 },
267 "datasection" => {
268 },
269 "data" => {
270 "perl" => '($value)? " -data" : ""',
271 },
272 "graph" => {
273 "perl" => '($value)? " -graph=$value" : ""',
274 },
275 "outfile" => {
276 "perl" => '($value)? " -outfile=$value" : ""',
277 },
278 "gap" => {
279 "perl" => '(defined $value && $value != $vdef)? " -gap=$value" : ""',
280 },
281 "boxit" => {
282 "perl" => '($value)? "" : " -noboxit"',
283 },
284 "dumpfeat" => {
285 "perl" => '($value)? " -dumpfeat" : ""',
286 },
287 "format" => {
288 "perl" => '($value && $value ne $vdef)? " -format=$value" : ""',
289 },
290 "ext" => {
291 "perl" => '($value && $value ne $vdef)? " -ext=$value" : ""',
292 },
293 "auto" => {
294 "perl" => '" -auto -stdout"',
295 },
296 "psouput" => {
297 "perl" => '" -goutfile=polydot"',
298 },
299 "psresults" => {
300 },
301 "metaresults" => {
302 },
303 "dataresults" => {
304 },
305 "pngresults" => {
306 },
307 "polydot" => {
308 "perl" => '"polydot"',
309 }
310
311 };
312
313 $self->{FILENAMES} = {
314 "psresults" => '*.ps',
315 "metaresults" => '*.meta',
316 "dataresults" => '*.dat',
317 "pngresults" => '*.png *.2 *.3',
318
319 };
320
321 $self->{SEQFMT} = {
322 "sequences" => [8],
323
324 };
325
326 $self->{GROUP} = {
327 "init" => -10,
328 "sequences" => 1,
329 "wordsize" => 2,
330 "data" => 3,
331 "graph" => 4,
332 "outfile" => 5,
333 "gap" => 6,
334 "boxit" => 7,
335 "dumpfeat" => 8,
336 "format" => 9,
337 "ext" => 10,
338 "auto" => 11,
339 "psouput" => 100,
340 "polydot" => 0
341
342 };
343
344 $self->{BY_GROUP_PARAMETERS} = [
345 "init",
346 "input",
347 "polydot",
348 "required",
349 "datasection",
350 "output",
351 "psresults",
352 "metaresults",
353 "dataresults",
354 "pngresults",
355 "sequences",
356 "wordsize",
357 "data",
358 "graph",
359 "outfile",
360 "gap",
361 "boxit",
362 "dumpfeat",
363 "format",
364 "ext",
365 "auto",
366 "psouput",
367
368 ];
369
370 $self->{SIZE} = {
371
372 };
373
374 $self->{ISHIDDEN} = {
375 "init" => 1,
376 "input" => 0,
377 "sequences" => 0,
378 "required" => 0,
379 "wordsize" => 0,
380 "output" => 0,
381 "datasection" => 0,
382 "data" => 0,
383 "graph" => 0,
384 "outfile" => 0,
385 "gap" => 0,
386 "boxit" => 0,
387 "dumpfeat" => 0,
388 "format" => 0,
389 "ext" => 0,
390 "auto" => 1,
391 "psouput" => 1,
392 "psresults" => 0,
393 "metaresults" => 0,
394 "dataresults" => 0,
395 "pngresults" => 0,
396 "polydot" => 1
397
398 };
399
400 $self->{ISCOMMAND} = {
401 "init" => 0,
402 "input" => 0,
403 "sequences" => 0,
404 "required" => 0,
405 "wordsize" => 0,
406 "output" => 0,
407 "datasection" => 0,
408 "data" => 0,
409 "graph" => 0,
410 "outfile" => 0,
411 "gap" => 0,
412 "boxit" => 0,
413 "dumpfeat" => 0,
414 "format" => 0,
415 "ext" => 0,
416 "auto" => 0,
417 "psouput" => 0,
418 "psresults" => 0,
419 "metaresults" => 0,
420 "dataresults" => 0,
421 "pngresults" => 0,
422
423 };
424
425 $self->{ISMANDATORY} = {
426 "init" => 0,
427 "input" => 0,
428 "sequences" => 1,
429 "required" => 0,
430 "wordsize" => 1,
431 "output" => 0,
432 "datasection" => 0,
433 "data" => 0,
434 "graph" => 0,
435 "outfile" => 0,
436 "gap" => 0,
437 "boxit" => 0,
438 "dumpfeat" => 0,
439 "format" => 0,
440 "ext" => 0,
441 "auto" => 0,
442 "psouput" => 0,
443 "psresults" => 0,
444 "metaresults" => 0,
445 "dataresults" => 0,
446 "pngresults" => 0,
447
448 };
449
450 $self->{PROMPT} = {
451 "init" => "",
452 "input" => "input Section",
453 "sequences" => "Sequences file to be read in (-sequences)",
454 "required" => "required Section",
455 "wordsize" => "Word size (-wordsize)",
456 "output" => "output Section",
457 "datasection" => "data Section",
458 "data" => "Display as data (-data)",
459 "graph" => "graph [device to be displayed on] (-graph)",
460 "outfile" => "outfile (-outfile)",
461 "gap" => "Gap (in residues) between dotplots (-gap)",
462 "boxit" => "Draw a box around each dotplot (-boxit)",
463 "dumpfeat" => "Dump all matches as feature files (-dumpfeat)",
464 "format" => "format to Dump out as (-format)",
465 "ext" => "Extension for feature file (-ext)",
466 "auto" => "",
467 "psouput" => "",
468 "psresults" => "",
469 "metaresults" => "",
470 "dataresults" => "",
471 "pngresults" => "",
472
473 };
474
475 $self->{ISSTANDOUT} = {
476 "init" => 0,
477 "input" => 0,
478 "sequences" => 0,
479 "required" => 0,
480 "wordsize" => 0,
481 "output" => 0,
482 "datasection" => 0,
483 "data" => 0,
484 "graph" => 0,
485 "outfile" => 0,
486 "gap" => 0,
487 "boxit" => 0,
488 "dumpfeat" => 0,
489 "format" => 0,
490 "ext" => 0,
491 "auto" => 0,
492 "psouput" => 0,
493 "psresults" => 0,
494 "metaresults" => 0,
495 "dataresults" => 0,
496 "pngresults" => 0,
497
498 };
499
500 $self->{VLIST} = {
501
502 "input" => ['sequences',],
503 "required" => ['wordsize',],
504 "output" => ['datasection',],
505 "datasection" => ['data','graph','outfile',],
506 "graph" => ['x11','x11','hp7470','hp7470','postscript','postscript','cps','cps','hp7580','hp7580','null','null','data','data','colourps','colourps','text','text','none','none','tek4107t','tek4107t','tekt','tekt','xwindows','xwindows','hpgl','hpgl','xterm','xterm','meta','meta','ps','ps','tek','tek','png','png','tektronics','tektronics',],
507 };
508
509 $self->{FLIST} = {
510
511 };
512
513 $self->{SEPARATOR} = {
514
515 };
516
517 $self->{VDEF} = {
518 "wordsize" => '6',
519 "data" => '0',
520 "graph" => 'postscript',
521 "gap" => '10',
522 "boxit" => '1',
523 "dumpfeat" => '0',
524 "format" => 'gff',
525 "ext" => 'gff',
526
527 };
528
529 $self->{PRECOND} = {
530 "init" => { "perl" => '1' },
531 "input" => { "perl" => '1' },
532 "sequences" => { "perl" => '1' },
533 "required" => { "perl" => '1' },
534 "wordsize" => { "perl" => '1' },
535 "output" => { "perl" => '1' },
536 "datasection" => { "perl" => '1' },
537 "data" => { "perl" => '1' },
538 "graph" => {
539 "acd" => '@(!$(data))',
540 },
541 "outfile" => {
542 "perl" => '$data',
543 "acd" => '$data',
544 },
545 "gap" => { "perl" => '1' },
546 "boxit" => { "perl" => '1' },
547 "dumpfeat" => { "perl" => '1' },
548 "format" => { "perl" => '1' },
549 "ext" => { "perl" => '1' },
550 "auto" => { "perl" => '1' },
551 "psouput" => {
552 "perl" => '$graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" || $graph eq "png"',
553 },
554 "psresults" => {
555 "perl" => '$graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps"',
556 },
557 "metaresults" => {
558 "perl" => '$graph eq "meta"',
559 },
560 "dataresults" => {
561 "perl" => '$graph eq "data"',
562 },
563 "pngresults" => {
564 "perl" => '$graph eq "png"',
565 },
566
567 };
568
569 $self->{CTRL} = {
570
571 };
572
573 $self->{PIPEOUT} = {
574
575 };
576
577 $self->{WITHPIPEOUT} = {
578
579 };
580
581 $self->{PIPEIN} = {
582 "sequences" => {
583 "seqsfile" => '1',
584 },
585
586 };
587
588 $self->{WITHPIPEIN} = {
589
590 };
591
592 $self->{ISCLEAN} = {
593 "init" => 0,
594 "input" => 0,
595 "sequences" => 0,
596 "required" => 0,
597 "wordsize" => 0,
598 "output" => 0,
599 "datasection" => 0,
600 "data" => 0,
601 "graph" => 0,
602 "outfile" => 0,
603 "gap" => 0,
604 "boxit" => 0,
605 "dumpfeat" => 0,
606 "format" => 0,
607 "ext" => 0,
608 "auto" => 0,
609 "psouput" => 0,
610 "psresults" => 0,
611 "metaresults" => 0,
612 "dataresults" => 0,
613 "pngresults" => 0,
614
615 };
616
617 $self->{ISSIMPLE} = {
618 "init" => 0,
619 "input" => 0,
620 "sequences" => 1,
621 "required" => 0,
622 "wordsize" => 1,
623 "output" => 0,
624 "datasection" => 0,
625 "data" => 0,
626 "graph" => 0,
627 "outfile" => 0,
628 "gap" => 0,
629 "boxit" => 0,
630 "dumpfeat" => 0,
631 "format" => 0,
632 "ext" => 0,
633 "auto" => 0,
634 "psouput" => 0,
635 "psresults" => 0,
636 "metaresults" => 0,
637 "dataresults" => 0,
638 "pngresults" => 0,
639
640 };
641
642 $self->{PARAMFILE} = {
643
644 };
645
646 $self->{COMMENT} = {
647 "sequences" => [
648 "File containing a sequence alignment",
649 ],
650 "data" => [
651 "Output the match data to a file instead of plotting it",
652 ],
653 "gap" => [
654 "This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output.",
655 ],
656
657 };
658
659 $self->{SCALEMIN} = {
660
661 };
662
663 $self->{SCALEMAX} = {
664
665 };
666
667 $self->{SCALEINC} = {
668
669 };
670
671 $self->{INFO} = {
672
673 };
674
675 # -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/polydot.pm
676
677
678
679 $self->_init_params(@params);
680
681 return $self;
682 }
683
684
685
686 1; # Needed to keep compiler happy
687
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