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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-09-03 11:00:03 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20090903110003-11of27rxner5vnl9
Tags: 1.6.1-1
http://bugs.debian.org/541274
* New upstream release.
* debian/patches/10-wrong-path-for-interpreter.patch: removed
  (fixed upstream).
* debian/watch updated (bioperl -> BioPerl).
* debian/rules refreshed with dh-make-perl 0.53.
  - Disabled installation of examples (removed upstream).
  - Removed the correction of file permission of Pise documentation
    (removed upstream).
  - Removed patching facilities (no patches anymore).
  - Disabled tests as I experience failures with t/Eponine.t despite
    this program is not installed.
* debian/copyright:
  - Removed vanity lines about debianization and debian copyright.
  - Incremented years to 2009.
  - Updated to latest experimentation of the machine-readable license summary.
* debian/control:
  - Incremented Standards-Version to reflect conformance on new Policy
    (dropped versionned build-dependancy on Perl).
  - Removed build-dependancy on quilt (no patches anymore).
  - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0.
  - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl,
    libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES.
  - Build-depends on libarray-compare-perl and libtree-dagnode-perl
    (otherwise tests fail). 
  - Depend on amap-align instead of amap (Closes: #541274).

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Bio/Tools/Run/PiseApplication/isochore.pm
1
 
# $Id: isochore.pm,v 1.6 2006/07/04 22:23:34 mauricio Exp $
2
 
# BioPerl module for Bio::Tools::Run::PiseApplication::isochore
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::isochore
13
 
 
14
 
=head1 SYNOPSIS
15
 
 
16
 
  #
17
 
 
18
 
=head1 DESCRIPTION
19
 
 
20
 
Bio::Tools::Run::PiseApplication::isochore
21
 
 
22
 
      Bioperl class for:
23
 
 
24
 
        ISOCHORE        Plots isochores in large DNA sequences (EMBOSS)
25
 
 
26
 
 
27
 
      Parameters: 
28
 
 
29
 
        (see also:
30
 
          http://bioweb.pasteur.fr/seqanal/interfaces/isochore.html 
31
 
         for available values):
32
 
 
33
 
 
34
 
                isochore (String)
35
 
 
36
 
                init (String)
37
 
 
38
 
                sequence (Sequence)
39
 
                        sequence -- dna [single sequence] (-sequence)
40
 
                        pipe: seqfile
41
 
 
42
 
                window (Integer)
43
 
                        Window size (-window)
44
 
 
45
 
                shift (Integer)
46
 
                        Shift increment (-shift)
47
 
 
48
 
                out (OutFile)
49
 
                        out (-out)
50
 
 
51
 
                graph (Excl)
52
 
                        graph (-graph)
53
 
 
54
 
                auto (String)
55
 
 
56
 
                psouput (String)
57
 
 
58
 
=head1 FEEDBACK
59
 
 
60
 
=head2 Mailing Lists
61
 
 
62
 
User feedback is an integral part of the evolution of this and other
63
 
Bioperl modules. Send your comments and suggestions preferably to
64
 
the Bioperl mailing list.  Your participation is much appreciated.
65
 
 
66
 
  bioperl-l@bioperl.org                  - General discussion
67
 
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
68
 
 
69
 
=head2 Reporting Bugs
70
 
 
71
 
Report bugs to the Bioperl bug tracking system to help us keep track
72
 
of the bugs and their resolution. Bug reports can be submitted via the
73
 
web:
74
 
 
75
 
  http://bugzilla.open-bio.org/
76
 
 
77
 
=head1 AUTHOR
78
 
 
79
 
Catherine Letondal (letondal@pasteur.fr)
80
 
 
81
 
=head1 COPYRIGHT
82
 
 
83
 
Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
84
 
All Rights Reserved.
85
 
 
86
 
This module is free software; you can redistribute it and/or modify
87
 
it under the same terms as Perl itself.
88
 
 
89
 
=head1 DISCLAIMER
90
 
 
91
 
This software is provided "as is" without warranty of any kind.
92
 
 
93
 
=head1 SEE ALSO
94
 
 
95
 
=over
96
 
 
97
 
=item *
98
 
 
99
 
http://bioweb.pasteur.fr/seqanal/interfaces/isochore.html
100
 
 
101
 
=item *
102
 
 
103
 
Bio::Tools::Run::PiseApplication
104
 
 
105
 
=item *
106
 
 
107
 
Bio::Tools::Run::AnalysisFactory::Pise
108
 
 
109
 
=item *
110
 
 
111
 
Bio::Tools::Run::PiseJob
112
 
 
113
 
=back
114
 
 
115
 
=cut
116
 
 
117
 
#'
118
 
package Bio::Tools::Run::PiseApplication::isochore;
119
 
 
120
 
use vars qw(@ISA);
121
 
use strict;
122
 
use Bio::Tools::Run::PiseApplication;
123
 
 
124
 
@ISA = qw(Bio::Tools::Run::PiseApplication);
125
 
 
126
 
=head2 new
127
 
 
128
 
 Title   : new()
129
 
 Usage   : my $isochore = Bio::Tools::Run::PiseApplication::isochore->new($location, $email, @params);
130
 
 Function: Creates a Bio::Tools::Run::PiseApplication::isochore object.
131
 
           This method should not be used directly, but rather by 
132
 
           a Bio::Tools::Run::AnalysisFactory::Pise instance.
133
 
           my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
134
 
           my $isochore = $factory->program('isochore');
135
 
 Example : -
136
 
 Returns : An instance of Bio::Tools::Run::PiseApplication::isochore.
137
 
 
138
 
=cut
139
 
 
140
 
sub new {
141
 
    my ($class, $location, $email, @params) = @_;
142
 
    my $self = $class->SUPER::new($location, $email);
143
 
 
144
 
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/isochore.pm
145
 
 
146
 
    $self->{COMMAND}   = "isochore";
147
 
    $self->{VERSION}   = "5.a";
148
 
    $self->{TITLE}   = "ISOCHORE";
149
 
 
150
 
    $self->{DESCRIPTION}   = "Plots isochores in large DNA sequences (EMBOSS)";
151
 
 
152
 
    $self->{OPT_EMAIL}   = 0;
153
 
 
154
 
    $self->{CATEGORIES}   =  [  
155
 
 
156
 
         "nucleic:composition",
157
 
  ];
158
 
 
159
 
    $self->{DOCLINK}   = "http://www.uk.embnet.org/Software/EMBOSS/Apps/isochore.html";
160
 
 
161
 
    $self->{_INTERFACE_STANDOUT} = undef;
162
 
    $self->{_STANDOUT_FILE} = undef;
163
 
 
164
 
    $self->{TOP_PARAMETERS}  = [ 
165
 
        "isochore",
166
 
        "init",
167
 
        "input",
168
 
        "advanced",
169
 
        "output",
170
 
        "auto",
171
 
        "psouput",
172
 
        "psresults",
173
 
        "metaresults",
174
 
        "dataresults",
175
 
        "pngresults",
176
 
 
177
 
    ];
178
 
 
179
 
    $self->{PARAMETERS_ORDER}  = [
180
 
        "isochore",
181
 
        "init",
182
 
        "input",        # input Section
183
 
        "sequence",     # sequence -- dna [single sequence] (-sequence)
184
 
        "advanced",     # advanced Section
185
 
        "window",       # Window size (-window)
186
 
        "shift",        # Shift increment (-shift)
187
 
        "output",       # output Section
188
 
        "out",  # out (-out)
189
 
        "graph",        # graph (-graph)
190
 
        "auto",
191
 
        "psouput",
192
 
        "psresults",
193
 
        "metaresults",
194
 
        "dataresults",
195
 
        "pngresults",
196
 
 
197
 
    ];
198
 
 
199
 
    $self->{TYPE}  = {
200
 
        "isochore" => 'String',
201
 
        "init" => 'String',
202
 
        "input" => 'Paragraph',
203
 
        "sequence" => 'Sequence',
204
 
        "advanced" => 'Paragraph',
205
 
        "window" => 'Integer',
206
 
        "shift" => 'Integer',
207
 
        "output" => 'Paragraph',
208
 
        "out" => 'OutFile',
209
 
        "graph" => 'Excl',
210
 
        "auto" => 'String',
211
 
        "psouput" => 'String',
212
 
        "psresults" => 'Results',
213
 
        "metaresults" => 'Results',
214
 
        "dataresults" => 'Results',
215
 
        "pngresults" => 'Results',
216
 
 
217
 
    };
218
 
 
219
 
    $self->{FORMAT}  = {
220
 
        "init" => {
221
 
                "perl" => ' "" ',
222
 
        },
223
 
        "input" => {
224
 
        },
225
 
        "sequence" => {
226
 
                "perl" => '" -sequence=$value -sformat=fasta"',
227
 
        },
228
 
        "advanced" => {
229
 
        },
230
 
        "window" => {
231
 
                "perl" => '(defined $value && $value != $vdef)? " -window=$value" : ""',
232
 
        },
233
 
        "shift" => {
234
 
                "perl" => '(defined $value && $value != $vdef)? " -shift=$value" : ""',
235
 
        },
236
 
        "output" => {
237
 
        },
238
 
        "out" => {
239
 
                "perl" => '" -out=$value"',
240
 
        },
241
 
        "graph" => {
242
 
                "perl" => '($value)? " -graph=$value" : ""',
243
 
        },
244
 
        "auto" => {
245
 
                "perl" => '" -auto -stdout"',
246
 
        },
247
 
        "psouput" => {
248
 
                "perl" => '" -goutfile=isochore"',
249
 
        },
250
 
        "psresults" => {
251
 
        },
252
 
        "metaresults" => {
253
 
        },
254
 
        "dataresults" => {
255
 
        },
256
 
        "pngresults" => {
257
 
        },
258
 
        "isochore" => {
259
 
                "perl" => '"isochore"',
260
 
        }
261
 
 
262
 
    };
263
 
 
264
 
    $self->{FILENAMES}  = {
265
 
        "psresults" => '*.ps',
266
 
        "metaresults" => '*.meta',
267
 
        "dataresults" => '*.dat',
268
 
        "pngresults" => '*.png *.2 *.3',
269
 
 
270
 
    };
271
 
 
272
 
    $self->{SEQFMT}  = {
273
 
        "sequence" => [8],
274
 
 
275
 
    };
276
 
 
277
 
    $self->{GROUP}  = {
278
 
        "init" => -10,
279
 
        "sequence" => 1,
280
 
        "window" => 2,
281
 
        "shift" => 3,
282
 
        "out" => 4,
283
 
        "graph" => 5,
284
 
        "auto" => 6,
285
 
        "psouput" => 100,
286
 
        "isochore" => 0
287
 
 
288
 
    };
289
 
 
290
 
    $self->{BY_GROUP_PARAMETERS}  = [
291
 
        "init",
292
 
        "input",
293
 
        "isochore",
294
 
        "advanced",
295
 
        "output",
296
 
        "psresults",
297
 
        "metaresults",
298
 
        "dataresults",
299
 
        "pngresults",
300
 
        "sequence",
301
 
        "window",
302
 
        "shift",
303
 
        "out",
304
 
        "graph",
305
 
        "auto",
306
 
        "psouput",
307
 
 
308
 
    ];
309
 
 
310
 
    $self->{SIZE}  = {
311
 
 
312
 
    };
313
 
 
314
 
    $self->{ISHIDDEN}  = {
315
 
        "init" => 1,
316
 
        "input" => 0,
317
 
        "sequence" => 0,
318
 
        "advanced" => 0,
319
 
        "window" => 0,
320
 
        "shift" => 0,
321
 
        "output" => 0,
322
 
        "out" => 0,
323
 
        "graph" => 0,
324
 
        "auto" => 1,
325
 
        "psouput" => 1,
326
 
        "psresults" => 0,
327
 
        "metaresults" => 0,
328
 
        "dataresults" => 0,
329
 
        "pngresults" => 0,
330
 
        "isochore" => 1
331
 
 
332
 
    };
333
 
 
334
 
    $self->{ISCOMMAND}  = {
335
 
        "init" => 0,
336
 
        "input" => 0,
337
 
        "sequence" => 0,
338
 
        "advanced" => 0,
339
 
        "window" => 0,
340
 
        "shift" => 0,
341
 
        "output" => 0,
342
 
        "out" => 0,
343
 
        "graph" => 0,
344
 
        "auto" => 0,
345
 
        "psouput" => 0,
346
 
        "psresults" => 0,
347
 
        "metaresults" => 0,
348
 
        "dataresults" => 0,
349
 
        "pngresults" => 0,
350
 
 
351
 
    };
352
 
 
353
 
    $self->{ISMANDATORY}  = {
354
 
        "init" => 0,
355
 
        "input" => 0,
356
 
        "sequence" => 1,
357
 
        "advanced" => 0,
358
 
        "window" => 0,
359
 
        "shift" => 0,
360
 
        "output" => 0,
361
 
        "out" => 1,
362
 
        "graph" => 0,
363
 
        "auto" => 0,
364
 
        "psouput" => 0,
365
 
        "psresults" => 0,
366
 
        "metaresults" => 0,
367
 
        "dataresults" => 0,
368
 
        "pngresults" => 0,
369
 
 
370
 
    };
371
 
 
372
 
    $self->{PROMPT}  = {
373
 
        "init" => "",
374
 
        "input" => "input Section",
375
 
        "sequence" => "sequence -- dna [single sequence] (-sequence)",
376
 
        "advanced" => "advanced Section",
377
 
        "window" => "Window size (-window)",
378
 
        "shift" => "Shift increment (-shift)",
379
 
        "output" => "output Section",
380
 
        "out" => "out (-out)",
381
 
        "graph" => "graph (-graph)",
382
 
        "auto" => "",
383
 
        "psouput" => "",
384
 
        "psresults" => "",
385
 
        "metaresults" => "",
386
 
        "dataresults" => "",
387
 
        "pngresults" => "",
388
 
 
389
 
    };
390
 
 
391
 
    $self->{ISSTANDOUT}  = {
392
 
        "init" => 0,
393
 
        "input" => 0,
394
 
        "sequence" => 0,
395
 
        "advanced" => 0,
396
 
        "window" => 0,
397
 
        "shift" => 0,
398
 
        "output" => 0,
399
 
        "out" => 0,
400
 
        "graph" => 0,
401
 
        "auto" => 0,
402
 
        "psouput" => 0,
403
 
        "psresults" => 0,
404
 
        "metaresults" => 0,
405
 
        "dataresults" => 0,
406
 
        "pngresults" => 0,
407
 
 
408
 
    };
409
 
 
410
 
    $self->{VLIST}  = {
411
 
 
412
 
        "input" => ['sequence',],
413
 
        "advanced" => ['window','shift',],
414
 
        "output" => ['out','graph',],
415
 
        "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',],
416
 
    };
417
 
 
418
 
    $self->{FLIST}  = {
419
 
 
420
 
    };
421
 
 
422
 
    $self->{SEPARATOR}  = {
423
 
 
424
 
    };
425
 
 
426
 
    $self->{VDEF}  = {
427
 
        "window" => '1000',
428
 
        "shift" => '100',
429
 
        "out" => 'out.out',
430
 
        "graph" => 'postscript',
431
 
 
432
 
    };
433
 
 
434
 
    $self->{PRECOND}  = {
435
 
        "init" => { "perl" => '1' },
436
 
        "input" => { "perl" => '1' },
437
 
        "sequence" => { "perl" => '1' },
438
 
        "advanced" => { "perl" => '1' },
439
 
        "window" => { "perl" => '1' },
440
 
        "shift" => { "perl" => '1' },
441
 
        "output" => { "perl" => '1' },
442
 
        "out" => { "perl" => '1' },
443
 
        "graph" => { "perl" => '1' },
444
 
        "auto" => { "perl" => '1' },
445
 
        "psouput" => {
446
 
                "perl" => '$graph eq "postscript" || $graph eq "ps" || $graph eq "colourps"  || $graph eq "cps" || $graph eq "png"',
447
 
        },
448
 
        "psresults" => {
449
 
                "perl" => '$graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps"',
450
 
        },
451
 
        "metaresults" => {
452
 
                "perl" => '$graph eq "meta"',
453
 
        },
454
 
        "dataresults" => {
455
 
                "perl" => '$graph eq "data"',
456
 
        },
457
 
        "pngresults" => {
458
 
                "perl" => '$graph eq "png"',
459
 
        },
460
 
 
461
 
    };
462
 
 
463
 
    $self->{CTRL}  = {
464
 
 
465
 
    };
466
 
 
467
 
    $self->{PIPEOUT}  = {
468
 
 
469
 
    };
470
 
 
471
 
    $self->{WITHPIPEOUT}  = {
472
 
 
473
 
    };
474
 
 
475
 
    $self->{PIPEIN}  = {
476
 
        "sequence" => {
477
 
                 "seqfile" => '1',
478
 
        },
479
 
 
480
 
    };
481
 
 
482
 
    $self->{WITHPIPEIN}  = {
483
 
 
484
 
    };
485
 
 
486
 
    $self->{ISCLEAN}  = {
487
 
        "init" => 0,
488
 
        "input" => 0,
489
 
        "sequence" => 0,
490
 
        "advanced" => 0,
491
 
        "window" => 0,
492
 
        "shift" => 0,
493
 
        "output" => 0,
494
 
        "out" => 0,
495
 
        "graph" => 0,
496
 
        "auto" => 0,
497
 
        "psouput" => 0,
498
 
        "psresults" => 0,
499
 
        "metaresults" => 0,
500
 
        "dataresults" => 0,
501
 
        "pngresults" => 0,
502
 
 
503
 
    };
504
 
 
505
 
    $self->{ISSIMPLE}  = {
506
 
        "init" => 0,
507
 
        "input" => 0,
508
 
        "sequence" => 1,
509
 
        "advanced" => 0,
510
 
        "window" => 0,
511
 
        "shift" => 0,
512
 
        "output" => 0,
513
 
        "out" => 1,
514
 
        "graph" => 0,
515
 
        "auto" => 0,
516
 
        "psouput" => 0,
517
 
        "psresults" => 0,
518
 
        "metaresults" => 0,
519
 
        "dataresults" => 0,
520
 
        "pngresults" => 0,
521
 
 
522
 
    };
523
 
 
524
 
    $self->{PARAMFILE}  = {
525
 
 
526
 
    };
527
 
 
528
 
    $self->{COMMENT}  = {
529
 
 
530
 
    };
531
 
 
532
 
    $self->{SCALEMIN}  = {
533
 
 
534
 
    };
535
 
 
536
 
    $self->{SCALEMAX}  = {
537
 
 
538
 
    };
539
 
 
540
 
    $self->{SCALEINC}  = {
541
 
 
542
 
    };
543
 
 
544
 
    $self->{INFO}  = {
545
 
 
546
 
    };
547
 
 
548
 
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/isochore.pm
549
 
 
550
 
 
551
 
 
552
 
    $self->_init_params(@params);
553
 
 
554
 
    return $self;
555
 
}
556
 
 
557
 
 
558
 
 
559
 
1; # Needed to keep compiler happy
560