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Move Pise modules over to bioperl-pise

svn path=/bioperl-pise/trunk/; revision=15349
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commit 4f47994c1c00f22e15452b7548ef6a6a2e16c1da 1 parent b2c081e
authored January 13, 2009

Showing 68 changed files with 43,650 additions and 0 deletions. Show diff stats Hide diff stats

  1. 454  Bio/Tools/Run/PiseApplication/CSR.pm
  2. 1,294  Bio/Tools/Run/PiseApplication/Puzzle.pm
  3. 662  Bio/Tools/Run/PiseApplication/abiview.pm
  4. 420  Bio/Tools/Run/PiseApplication/addquart.pm
  5. 621  Bio/Tools/Run/PiseApplication/align2model.pm
  6. 396  Bio/Tools/Run/PiseApplication/alistat.pm
  7. 433  Bio/Tools/Run/PiseApplication/antigenic.pm
  8. 608  Bio/Tools/Run/PiseApplication/assp.pm
  9. 459  Bio/Tools/Run/PiseApplication/backtranseq.pm
  10. 1,450  Bio/Tools/Run/PiseApplication/bambe.pm
  11. 580  Bio/Tools/Run/PiseApplication/banana.pm
  12. 355  Bio/Tools/Run/PiseApplication/bionj.pm
  13. 512  Bio/Tools/Run/PiseApplication/biosed.pm
  14. 816  Bio/Tools/Run/PiseApplication/bl2seq.pm
  15. 1,381  Bio/Tools/Run/PiseApplication/blast2.pm
  16. 742  Bio/Tools/Run/PiseApplication/blimps.pm
  17. 572  Bio/Tools/Run/PiseApplication/blimps_block.pm
  18. 657  Bio/Tools/Run/PiseApplication/blimps_matrix.pm
  19. 1,157  Bio/Tools/Run/PiseApplication/boxshade.pm
  20. 452  Bio/Tools/Run/PiseApplication/btwisted.pm
  21. 434  Bio/Tools/Run/PiseApplication/cai.pm
  22. 316  Bio/Tools/Run/PiseApplication/cap.pm
  23. 659  Bio/Tools/Run/PiseApplication/cds.pm
  24. 530  Bio/Tools/Run/PiseApplication/chaos.pm
  25. 583  Bio/Tools/Run/PiseApplication/charge.pm
  26. 554  Bio/Tools/Run/PiseApplication/checktrans.pm
  27. 452  Bio/Tools/Run/PiseApplication/chips.pm
  28. 822  Bio/Tools/Run/PiseApplication/cirdna.pm
  29. 862  Bio/Tools/Run/PiseApplication/clique.pm
  30. 1,840  Bio/Tools/Run/PiseApplication/clustalw.pm
  31. 445  Bio/Tools/Run/PiseApplication/clustalw_convert.pm
  32. 414  Bio/Tools/Run/PiseApplication/codcmp.pm
  33. 497  Bio/Tools/Run/PiseApplication/coderet.pm
  34. 599  Bio/Tools/Run/PiseApplication/codnocod.pm
  35. 526  Bio/Tools/Run/PiseApplication/codontree.pm
  36. 953  Bio/Tools/Run/PiseApplication/codonw.pm
  37. 463  Bio/Tools/Run/PiseApplication/comalign.pm
  38. 573  Bio/Tools/Run/PiseApplication/combat.pm
  39. 565  Bio/Tools/Run/PiseApplication/compseq.pm
  40. 336  Bio/Tools/Run/PiseApplication/con_filter.pm
  41. 441  Bio/Tools/Run/PiseApplication/confmat.pm
  42. 546  Bio/Tools/Run/PiseApplication/cons.pm
  43. 640  Bio/Tools/Run/PiseApplication/consense.pm
  44. 858  Bio/Tools/Run/PiseApplication/consensus.pm
  45. 743  Bio/Tools/Run/PiseApplication/cpgplot.pm
  46. 478  Bio/Tools/Run/PiseApplication/cpgreport.pm
  47. 433  Bio/Tools/Run/PiseApplication/cusp.pm
  48. 481  Bio/Tools/Run/PiseApplication/cutseq.pm
  49. 860  Bio/Tools/Run/PiseApplication/dan.pm
  50. 568  Bio/Tools/Run/PiseApplication/dca.pm
  51. 466  Bio/Tools/Run/PiseApplication/decorate.pm
  52. 423  Bio/Tools/Run/PiseApplication/degapseq.pm
  53. 496  Bio/Tools/Run/PiseApplication/descseq.pm
  54. 499  Bio/Tools/Run/PiseApplication/dialign2.pm
  55. 560  Bio/Tools/Run/PiseApplication/diffseq.pm
  56. 534  Bio/Tools/Run/PiseApplication/digest.pm
  57. 578  Bio/Tools/Run/PiseApplication/distmat.pm
  58. 510  Bio/Tools/Run/PiseApplication/distquart.pm
  59. 993  Bio/Tools/Run/PiseApplication/dnadist.pm
  60. 1,246  Bio/Tools/Run/PiseApplication/dnapars.pm
  61. 1,064  Bio/Tools/Run/PiseApplication/dollop.pm
  62. 508  Bio/Tools/Run/PiseApplication/domainer.pm
  63. 673  Bio/Tools/Run/PiseApplication/dotmatcher.pm
  64. 641  Bio/Tools/Run/PiseApplication/dotpath.pm
  65. 651  Bio/Tools/Run/PiseApplication/dottup.pm
  66. 924  Bio/Tools/Run/PiseApplication/drawgram.pm
  67. 392  Bio/Tools/Run/PiseApplication/drawpyr.pm
454  Bio/Tools/Run/PiseApplication/CSR.pm
... ...
@@ -0,0 +1,454 @@
  1
+
  2
+=head1 NAME
  3
+
  4
+Bio::Tools::Run::PiseApplication::CSR
  5
+
  6
+=head1 SYNOPSIS
  7
+
  8
+  #
  9
+
  10
+=head1 DESCRIPTION
  11
+
  12
+Bio::Tools::Run::PiseApplication::CSR
  13
+
  14
+      Bioperl class for:
  15
+
  16
+	CSR	Maximal Common 3D Substructure Searching (M.Petitjean)
  17
+
  18
+	References:
  19
+
  20
+		M.Petitjean, Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm. Comput.Chem.1998,22[6],pp.463-465. 
  21
+
  22
+
  23
+      Parameters:
  24
+
  25
+
  26
+		CSR (String)
  27
+
  28
+
  29
+		param (Results)
  30
+
  31
+
  32
+		endparams (String)
  33
+
  34
+
  35
+		pdbfile (InFile)
  36
+			File containing both molecules
  37
+			pipe: pdbfile
  38
+
  39
+		file_format (Excl)
  40
+			Input file format
  41
+
  42
+		imol1 (Integer)
  43
+			Position of the 1st molecule in the file (IMOL1)
  44
+
  45
+		imol2 (Integer)
  46
+			Position of the 2d molecule in the file (IMOL2)
  47
+
  48
+		itermx (Integer)
  49
+			How many iterations (ITERMX)
  50
+
  51
+		cutoff (Excl)
  52
+			Cutoff distance (CUT-OFF DIST)
  53
+
  54
+		substructure (OutFile)
  55
+
  56
+
  57
+		pdb_outfile (Results)
  58
+
  59
+			pipe: pdbfile
  60
+
  61
+=cut
  62
+
  63
+#'
  64
+package Bio::Tools::Run::PiseApplication::CSR;
  65
+
  66
+use vars qw(@ISA);
  67
+use strict;
  68
+use Bio::Tools::Run::PiseApplication;
  69
+
  70
+@ISA = qw(Bio::Tools::Run::PiseApplication);
  71
+
  72
+=head2 new
  73
+
  74
+ Title   : new()
  75
+ Usage   : my $CSR = Bio::Tools::Run::PiseApplication::CSR->new($remote, $email, @params);
  76
+ Function: Creates a Bio::Tools::Run::PiseApplication::CSR object.
  77
+           This method should not be used directly, but rather by 
  78
+           a Bio::Factory::Pise instance:
  79
+           my $factory = Bio::Factory::Pise->new(-email => 'me@myhome');
  80
+           my $CSR = $factory->program('CSR');
  81
+ Example :
  82
+ Returns : An instance of Bio::Tools::Run::PiseApplication::CSR.
  83
+
  84
+=cut
  85
+
  86
+sub new {
  87
+    my ($class, $remote, $email, @params) = @_;
  88
+    my $self = $class->SUPER::new($remote, $email);
  89
+
  90
+# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/CSR.pm
  91
+
  92
+    $self->{COMMAND}   = "CSR";
  93
+    $self->{VERSION}   = "5.a";
  94
+    $self->{TITLE}   = "CSR";
  95
+
  96
+    $self->{DESCRIPTION}   = "Maximal Common 3D Substructure Searching";
  97
+
  98
+    $self->{AUTHORS}   = "M.Petitjean";
  99
+
  100
+    $self->{REFERENCE}   = [
  101
+
  102
+         "M.Petitjean, Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm. Comput.Chem.1998,22[6],pp.463-465. ",
  103
+ ];
  104
+
  105
+    $self->{_INTERFACE_STANDOUT} = undef;
  106
+    $self->{_STANDOUT_FILE} = undef;
  107
+
  108
+    $self->{TOP_PARAMETERS}  = [ 
  109
+	"CSR",
  110
+	"param",
  111
+	"endparams",
  112
+	"pdbfile",
  113
+	"file_format",
  114
+	"imol1",
  115
+	"imol2",
  116
+	"itermx",
  117
+	"cutoff",
  118
+	"substructure",
  119
+	"pdb_outfile",
  120
+
  121
+    ];
  122
+
  123
+    $self->{PARAMETERS_ORDER}  = [
  124
+	"CSR",
  125
+	"param",
  126
+	"endparams",
  127
+	"pdbfile", 	# File containing both molecules
  128
+	"file_format", 	# Input file format
  129
+	"imol1", 	# Position of the 1st molecule in the file (IMOL1)
  130
+	"imol2", 	# Position of the 2d molecule in the file (IMOL2)
  131
+	"itermx", 	# How many iterations (ITERMX)
  132
+	"cutoff", 	# Cutoff distance (CUT-OFF DIST)
  133
+	"substructure",
  134
+	"pdb_outfile",
  135
+
  136
+    ];
  137
+
  138
+    $self->{TYPE}  = {
  139
+	"CSR" => 'String',
  140
+	"param" => 'Results',
  141
+	"endparams" => 'String',
  142
+	"pdbfile" => 'InFile',
  143
+	"file_format" => 'Excl',
  144
+	"imol1" => 'Integer',
  145
+	"imol2" => 'Integer',
  146
+	"itermx" => 'Integer',
  147
+	"cutoff" => 'Excl',
  148
+	"substructure" => 'OutFile',
  149
+	"pdb_outfile" => 'Results',
  150
+
  151
+    };
  152
+
  153
+    $self->{FORMAT}  = {
  154
+	"CSR" => {
  155
+		"perl" => ' "CSR < params" ',
  156
+	},
  157
+	"param" => {
  158
+	},
  159
+	"endparams" => {
  160
+		"perl" => '"\\n\\n"',
  161
+	},
  162
+	"pdbfile" => {
  163
+		"perl" => '"$value\\n"',
  164
+	},
  165
+	"file_format" => {
  166
+		"perl" => '"$value\\n"',
  167
+	},
  168
+	"imol1" => {
  169
+		"perl" => '"$value"',
  170
+	},
  171
+	"imol2" => {
  172
+		"perl" => '" $value"',
  173
+	},
  174
+	"itermx" => {
  175
+		"perl" => '" $value"',
  176
+	},
  177
+	"cutoff" => {
  178
+		"perl" => '" $value\\n"',
  179
+	},
  180
+	"substructure" => {
  181
+		"perl" => '"new_mol2.coord\\n"',
  182
+	},
  183
+	"pdb_outfile" => {
  184
+	},
  185
+
  186
+    };
  187
+
  188
+    $self->{FILENAMES}  = {
  189
+	"param" => 'params',
  190
+	"pdb_outfile" => 'new_mol2.coord',
  191
+
  192
+    };
  193
+
  194
+    $self->{SEQFMT}  = {
  195
+
  196
+    };
  197
+
  198
+    $self->{GROUP}  = {
  199
+	"CSR" => 0,
  200
+	"endparams" => 10,
  201
+	"pdbfile" => 2,
  202
+	"file_format" => 1,
  203
+	"imol1" => 4,
  204
+	"imol2" => 5,
  205
+	"itermx" => 6,
  206
+	"cutoff" => 7,
  207
+	"substructure" => 3,
  208
+
  209
+    };
  210
+
  211
+    $self->{BY_GROUP_PARAMETERS}  = [
  212
+	"CSR",
  213
+	"param",
  214
+	"pdb_outfile",
  215
+	"file_format",
  216
+	"pdbfile",
  217
+	"substructure",
  218
+	"imol1",
  219
+	"imol2",
  220
+	"itermx",
  221
+	"cutoff",
  222
+	"endparams",
  223
+
  224
+    ];
  225
+
  226
+    $self->{SIZE}  = {
  227
+
  228
+    };
  229
+
  230
+    $self->{ISHIDDEN}  = {
  231
+	"CSR" => 1,
  232
+	"param" => 0,
  233
+	"endparams" => 1,
  234
+	"pdbfile" => 0,
  235
+	"file_format" => 0,
  236
+	"imol1" => 0,
  237
+	"imol2" => 0,
  238
+	"itermx" => 0,
  239
+	"cutoff" => 0,
  240
+	"substructure" => 1,
  241
+	"pdb_outfile" => 0,
  242
+
  243
+    };
  244
+
  245
+    $self->{ISCOMMAND}  = {
  246
+	"CSR" => 1,
  247
+	"param" => 0,
  248
+	"endparams" => 0,
  249
+	"pdbfile" => 0,
  250
+	"file_format" => 0,
  251
+	"imol1" => 0,
  252
+	"imol2" => 0,
  253
+	"itermx" => 0,
  254
+	"cutoff" => 0,
  255
+	"substructure" => 0,
  256
+	"pdb_outfile" => 0,
  257
+
  258
+    };
  259
+
  260
+    $self->{ISMANDATORY}  = {
  261
+	"CSR" => 0,
  262
+	"param" => 0,
  263
+	"endparams" => 0,
  264
+	"pdbfile" => 1,
  265
+	"file_format" => 1,
  266
+	"imol1" => 1,
  267
+	"imol2" => 1,
  268
+	"itermx" => 1,
  269
+	"cutoff" => 1,
  270
+	"substructure" => 1,
  271
+	"pdb_outfile" => 0,
  272
+
  273
+    };
  274
+
  275
+    $self->{PROMPT}  = {
  276
+	"CSR" => "",
  277
+	"param" => "",
  278
+	"endparams" => "",
  279
+	"pdbfile" => "File containing both molecules",
  280
+	"file_format" => "Input file format",
  281
+	"imol1" => "Position of the 1st molecule in the file (IMOL1)",
  282
+	"imol2" => "Position of the 2d molecule in the file (IMOL2)",
  283
+	"itermx" => "How many iterations (ITERMX)",
  284
+	"cutoff" => "Cutoff distance (CUT-OFF DIST)",
  285
+	"substructure" => "",
  286
+	"pdb_outfile" => "",
  287
+
  288
+    };
  289
+
  290
+    $self->{ISSTANDOUT}  = {
  291
+	"CSR" => 0,
  292
+	"param" => 0,
  293
+	"endparams" => 0,
  294
+	"pdbfile" => 0,
  295
+	"file_format" => 0,
  296
+	"imol1" => 0,
  297
+	"imol2" => 0,
  298
+	"itermx" => 0,
  299
+	"cutoff" => 0,
  300
+	"substructure" => 0,
  301
+	"pdb_outfile" => 0,
  302
+
  303
+    };
  304
+
  305
+    $self->{VLIST}  = {
  306
+
  307
+	"file_format" => ['HIN','HIN: alchemy-type','MDL','MDL: Cambridge Crystallographic Model','ML2','ML2: Mol2 SYBYL','PDB','PDB: Protein Data Bank or Nucleic Acid Data Bank','BIO','BIO: Biosym (MSI)',],
  308
+	"cutoff" => ['1.2','1.2: for a protein','2','2: for an inorganic molecule','5','5: for a C-alpha backbone.',],
  309
+    };
  310
+
  311
+    $self->{FLIST}  = {
  312
+
  313
+    };
  314
+
  315
+    $self->{SEPARATOR}  = {
  316
+
  317
+    };
  318
+
  319
+    $self->{VDEF}  = {
  320
+	"file_format" => 'PDB',
  321
+	"imol1" => '1',
  322
+	"imol2" => '2',
  323
+	"itermx" => '200',
  324
+	"cutoff" => '1.2',
  325
+	"substructure" => 'new_mol2.coord',
  326
+
  327
+    };
  328
+
  329
+    $self->{PRECOND}  = {
  330
+	"CSR" => { "perl" => '1' },
  331
+	"param" => { "perl" => '1' },
  332
+	"endparams" => { "perl" => '1' },
  333
+	"pdbfile" => { "perl" => '1' },
  334
+	"file_format" => { "perl" => '1' },
  335
+	"imol1" => { "perl" => '1' },
  336
+	"imol2" => { "perl" => '1' },
  337
+	"itermx" => { "perl" => '1' },
  338
+	"cutoff" => { "perl" => '1' },
  339
+	"substructure" => { "perl" => '1' },
  340
+	"pdb_outfile" => { "perl" => '1' },
  341
+
  342
+    };
  343
+
  344
+    $self->{CTRL}  = {
  345
+
  346
+    };
  347
+
  348
+    $self->{PIPEOUT}  = {
  349
+	"pdb_outfile" => {
  350
+		 '1' => "pdbfile",
  351
+	},
  352
+
  353
+    };
  354
+
  355
+    $self->{WITHPIPEOUT}  = {
  356
+
  357
+    };
  358
+
  359
+    $self->{PIPEIN}  = {
  360
+	"pdbfile" => {
  361
+		 "pdbfile" => '$file_format eq "PDB"',
  362
+	},
  363
+
  364
+    };
  365
+
  366
+    $self->{WITHPIPEIN}  = {
  367
+
  368
+    };
  369
+
  370
+    $self->{ISCLEAN}  = {
  371
+	"CSR" => 0,
  372
+	"param" => 0,
  373
+	"endparams" => 0,
  374
+	"pdbfile" => 0,
  375
+	"file_format" => 0,
  376
+	"imol1" => 0,
  377
+	"imol2" => 0,
  378
+	"itermx" => 0,
  379
+	"cutoff" => 0,
  380
+	"substructure" => 0,
  381
+	"pdb_outfile" => 0,
  382
+
  383
+    };
  384
+
  385
+    $self->{ISSIMPLE}  = {
  386
+	"CSR" => 0,
  387
+	"param" => 0,
  388
+	"endparams" => 0,
  389
+	"pdbfile" => 1,
  390
+	"file_format" => 1,
  391
+	"imol1" => 1,
  392
+	"imol2" => 1,
  393
+	"itermx" => 1,
  394
+	"cutoff" => 0,
  395
+	"substructure" => 0,
  396
+	"pdb_outfile" => 0,
  397
+
  398
+    };
  399
+
  400
+    $self->{PARAMFILE}  = {
  401
+	"endparams" => "params",
  402
+	"pdbfile" => "params",
  403
+	"file_format" => "params",
  404
+	"imol1" => "params",
  405
+	"imol2" => "params",
  406
+	"itermx" => "params",
  407
+	"cutoff" => "params",
  408
+	"substructure" => "params",
  409
+
  410
+    };
  411
+
  412
+    $self->{COMMENT}  = {
  413
+	"pdbfile" => [
  414
+		"This file must contain BOTH molecules.",
  415
+		"See below the position parameters of each molecules.",
  416
+	],
  417
+	"itermx" => [
  418
+		"About 200 for a small molecule of less than 100 atoms, about 2000 for less than 1000 atoms, 20000 for more than 1000 atoms",
  419
+	],
  420
+	"cutoff" => [
  421
+		"This parameter does not change the results, it just saves memory and space.",
  422
+	],
  423
+
  424
+    };
  425
+
  426
+    $self->{SCALEMIN}  = {
  427
+
  428
+    };
  429
+
  430
+    $self->{SCALEMAX}  = {
  431
+
  432
+    };
  433
+
  434
+    $self->{SCALEINC}  = {
  435
+
  436
+    };
  437
+
  438
+    $self->{INFO}  = {
  439
+
  440
+    };
  441
+
  442
+# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/CSR.pm
  443
+
  444
+
  445
+
  446
+    $self->_init_params(@params);
  447
+
  448
+    return $self;
  449
+}
  450
+
  451
+
  452
+
  453
+1; # Needed to keep compiler happy
  454
+
1,294  Bio/Tools/Run/PiseApplication/Puzzle.pm
... ...
@@ -0,0 +1,1294 @@
  1
+# $Id$
  2
+# BioPerl module for Bio::Tools::Run::PiseApplication::Puzzle
  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::Puzzle
  13
+
  14
+=head1 SYNOPSIS
  15
+
  16
+  #
  17
+
  18
+=head1 DESCRIPTION
  19
+
  20
+Bio::Tools::Run::PiseApplication::Puzzle
  21
+
  22
+      Bioperl class for:
  23
+
  24
+	Puzzle	Tree reconstruction for sequences by quartet puzzling and maximum likelihood (Strimmer, von Haeseler)
  25
+
  26
+	References:
  27
+
  28
+		Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling:A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.
  29
+
  30
+
  31
+
  32
+      Parameters: 
  33
+
  34
+        (see also:
  35
+          http://bioweb.pasteur.fr/seqanal/interfaces/Puzzle.html 
  36
+         for available values):
  37
+
  38
+
  39
+		Puzzle (String)
  40
+
  41
+		stdinput (String)
  42
+
  43
+		confirm (String)
  44
+
  45
+		infile (Sequence)
  46
+			Alignement File
  47
+			pipe: readseq_ok_alig
  48
+
  49
+		seqtype (Excl)
  50
+			Is it a DNA or protein sequence
  51
+
  52
+		approximate (Switch)
  53
+			Approximate quartet likelihood (v)
  54
+
  55
+		puzzling_step (Integer)
  56
+			Number of puzzling steps (n)
  57
+
  58
+		protein_model (Excl)
  59
+			Model of substitution for protein (if no automatic guess) (m)
  60
+
  61
+		ratio (Float)
  62
+			Transition/transversion ratio (t)
  63
+
  64
+		GTR_acrate (Float)
  65
+			A-C rate (1)
  66
+
  67
+		GTR_agrate (Float)
  68
+			A-G rate (2)
  69
+
  70
+		GTR_atrate (Float)
  71
+			A-T rate (3)
  72
+
  73
+		GTR_cgrate (Float)
  74
+			C-G rate (4)
  75
+
  76
+		GTR_ctrate (Float)
  77
+			C-T rate (5)
  78
+
  79
+		GTR_gtrate (Float)
  80
+			G-T rate (6)
  81
+
  82
+		use_specified (Switch)
  83
+			Use specified values
  84
+
  85
+		a_freq (Float)
  86
+			pi(A)
  87
+
  88
+		c_freq (Float)
  89
+			pi(C)
  90
+
  91
+		g_freq (Float)
  92
+			pi(G)
  93
+
  94
+		dna_model (Excl)
  95
+			Model of substitution for DNA (m)
  96
+
  97
+		constrain_TN (Switch)
  98
+			Constrain TN model to F84 model (p)
  99
+
  100
+		f84_ratio (Float)
  101
+			Expected F84 Transition/transversion ratio
  102
+
  103
+		y_r (Float)
  104
+			Y/R transition parameter (r)
  105
+
  106
+		symmetrize_frequencies (Switch)
  107
+			Symmetrize doublet frequencies (s)
  108
+
  109
+		rate_heterogeneity (Excl)
  110
+			Model of rate heterogeneity (w)
  111
+
  112
+		alpha (Float)
  113
+			Gamma distribution parameter alpha (a)
  114
+
  115
+		gamma_number (Integer)
  116
+			Number of Gamma rate categories (c)
  117
+
  118
+		invariable (Float)
  119
+			Fraction of invariable sites (i)
  120
+
  121
+		user_tree (Switch)
  122
+			Tree search procedure: User tree (k)
  123
+
  124
+		tree_file (InFile)
  125
+			User Tree file
  126
+
  127
+		no_tree (Switch)
  128
+			Pairwise distances only (no tree) (k)
  129
+
  130
+		outgroup (Integer)
  131
+			Display as outgroup (o)
  132
+
  133
+		branch_length (Switch)
  134
+			Compute clocklike branch lengths (z)
  135
+
  136
+		estimates (Excl)
  137
+			Parameter estimates (e)
  138
+
  139
+		estimation_by (Excl)
  140
+			Parameter estimation by (x)
  141
+
  142
+		list_unresolved (Switch)
  143
+			List unresolved quartets (u)
  144
+
  145
+		list_trees (Switch)
  146
+			List puzzling step trees (j)
  147
+
  148
+=head1 FEEDBACK
  149
+
  150
+=head2 Mailing Lists
  151
+
  152
+User feedback is an integral part of the evolution of this and other
  153
+Bioperl modules. Send your comments and suggestions preferably to
  154
+the Bioperl mailing list.  Your participation is much appreciated.
  155
+
  156
+  bioperl-l@bioperl.org                  - General discussion
  157
+  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  158
+
  159
+=head2 Reporting Bugs
  160
+
  161
+Report bugs to the Bioperl bug tracking system to help us keep track
  162
+of the bugs and their resolution. Bug reports can be submitted via
  163
+the web:
  164
+
  165
+  http://bugzilla.open-bio.org/
  166
+
  167
+=head1 AUTHOR
  168
+
  169
+Catherine Letondal (letondal@pasteur.fr)
  170
+
  171
+=head1 COPYRIGHT
  172
+
  173
+Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
  174
+All Rights Reserved.
  175
+
  176
+This module is free software; you can redistribute it and/or modify
  177
+it under the same terms as Perl itself.
  178
+
  179
+=head1 DISCLAIMER
  180
+
  181
+This software is provided "as is" without warranty of any kind.
  182
+
  183
+=head1 SEE ALSO
  184
+
  185
+=over
  186
+
  187
+=item *
  188
+
  189
+http://bioweb.pasteur.fr/seqanal/interfaces/Puzzle.html
  190
+
  191
+=item *
  192
+
  193
+Bio::Tools::Run::PiseApplication
  194
+
  195
+=item *
  196
+
  197
+Bio::Tools::Run::AnalysisFactory::Pise
  198
+
  199
+=item *
  200
+
  201
+Bio::Tools::Run::PiseJob
  202
+
  203
+=back
  204
+
  205
+=cut
  206
+
  207
+#'
  208
+package Bio::Tools::Run::PiseApplication::Puzzle;
  209
+
  210
+use vars qw(@ISA);
  211
+use strict;
  212
+use Bio::Tools::Run::PiseApplication;
  213
+
  214
+@ISA = qw(Bio::Tools::Run::PiseApplication);
  215
+
  216
+=head2 new
  217
+
  218
+ Title   : new()
  219
+ Usage   : my $Puzzle = Bio::Tools::Run::PiseApplication::Puzzle->new($location, $email, @params);
  220
+ Function: Creates a Bio::Tools::Run::PiseApplication::Puzzle object.
  221
+           This method should not be used directly, but rather by 
  222
+           a Bio::Tools::Run::AnalysisFactory::Pise instance.
  223
+           my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
  224
+           my $Puzzle = $factory->program('Puzzle');
  225
+ Example : -
  226
+ Returns : An instance of Bio::Tools::Run::PiseApplication::Puzzle.
  227
+
  228
+=cut
  229
+
  230
+sub new {
  231
+    my ($class, $location, $email, @params) = @_;
  232
+    my $self = $class->SUPER::new($location, $email);
  233
+
  234
+# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/Puzzle.pm
  235
+
  236
+    $self->{COMMAND}   = "Puzzle";
  237
+    $self->{VERSION}   = "5.a";
  238
+    $self->{TITLE}   = "Puzzle";
  239
+
  240
+    $self->{DESCRIPTION}   = "Tree reconstruction for sequences by quartet puzzling and maximum likelihood";
  241
+
  242
+    $self->{OPT_EMAIL}   = 0;
  243
+
  244
+    $self->{CATEGORIES}   =  [  
  245
+
  246
+         "phylogeny",
  247
+  ];
  248
+
  249
+    $self->{AUTHORS}   = "Strimmer, von Haeseler";
  250
+
  251
+    $self->{REFERENCE}   = [
  252
+
  253
+         "Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling:A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.",
  254
+ ];
  255
+
  256
+    $self->{_INTERFACE_STANDOUT} = undef;
  257
+    $self->{_STANDOUT_FILE} = undef;
  258
+
  259
+    $self->{TOP_PARAMETERS}  = [ 
  260
+	"Puzzle",
  261
+	"stdinput",
  262
+	"confirm",
  263
+	"outfile",
  264
+	"outtree",
  265
+	"outdist",
  266
+	"params",
  267
+	"infile",
  268
+	"seqtype",
  269
+	"control_options",
  270
+	"dna_model",
  271
+	"constrain_TN",
  272
+	"f84_ratio",
  273
+	"y_r",
  274
+	"symmetrize_frequencies",
  275
+	"output_options",
  276
+
  277
+    ];
  278
+
  279
+    $self->{PARAMETERS_ORDER}  = [
  280
+	"Puzzle",
  281
+	"stdinput",
  282
+	"confirm",
  283
+	"outfile",
  284
+	"outtree",
  285
+	"outdist",
  286
+	"params",
  287
+	"infile", 	# Alignement File
  288
+	"seqtype", 	# Is it a DNA or protein sequence
  289
+	"control_options", 	# Control options
  290
+	"approximate", 	# Approximate quartet likelihood (v)
  291
+	"puzzling_step", 	# Number of puzzling steps (n)
  292
+	"protein_options", 	# Protein options
  293
+	"protein_model", 	# Model of substitution for protein (if no automatic guess) (m)
  294
+	"dna_options", 	# DNA options
  295
+	"ratio", 	# Transition/transversion ratio (t)
  296
+	"GTR_options", 	# GTR model rates
  297
+	"GTR_acrate", 	# A-C rate (1)
  298
+	"GTR_agrate", 	# A-G rate (2)
  299
+	"GTR_atrate", 	# A-T rate (3)
  300
+	"GTR_cgrate", 	# C-G rate (4)
  301
+	"GTR_ctrate", 	# C-T rate (5)
  302
+	"GTR_gtrate", 	# G-T rate (6)
  303
+	"nuc_freq", 	# Nucleotids frequencies (in %) (f)
  304
+	"use_specified", 	# Use specified values
  305
+	"a_freq", 	# pi(A)
  306
+	"c_freq", 	# pi(C)
  307
+	"g_freq", 	# pi(G)
  308
+	"dna_model", 	# Model of substitution for DNA (m)
  309
+	"constrain_TN", 	# Constrain TN model to F84 model (p)
  310
+	"f84_ratio", 	# Expected F84 Transition/transversion ratio
  311
+	"y_r", 	# Y/R transition parameter (r)
  312
+	"symmetrize_frequencies", 	# Symmetrize doublet frequencies (s)
  313
+	"rate_options", 	# Rate heterogeneity options
  314
+	"rate_heterogeneity", 	# Model of rate heterogeneity (w)
  315
+	"alpha", 	# Gamma distribution parameter alpha (a)
  316
+	"gamma_number", 	# Number of Gamma rate categories (c)
  317
+	"invariable", 	# Fraction of invariable sites (i)
  318
+	"user_tree_options", 	# User Tree options
  319
+	"user_tree", 	# Tree search procedure: User tree (k)
  320
+	"tree_file", 	# User Tree file
  321
+	"no_tree", 	# Pairwise distances only (no tree) (k)
  322
+	"output_options", 	# Output options
  323
+	"outgroup", 	# Display as outgroup (o)
  324
+	"branch_length", 	# Compute clocklike branch lengths (z)
  325
+	"estimates", 	# Parameter estimates (e)
  326
+	"estimation_by", 	# Parameter estimation by (x)
  327
+	"list_unresolved", 	# List unresolved quartets (u)
  328
+	"list_trees", 	# List puzzling step trees (j)
  329
+
  330
+    ];
  331
+
  332
+    $self->{TYPE}  = {
  333
+	"Puzzle" => 'String',
  334
+	"stdinput" => 'String',
  335
+	"confirm" => 'String',
  336
+	"outfile" => 'Results',
  337
+	"outtree" => 'Results',
  338
+	"outdist" => 'Results',
  339
+	"params" => 'Results',
  340
+	"infile" => 'Sequence',
  341
+	"seqtype" => 'Excl',
  342
+	"control_options" => 'Paragraph',
  343
+	"approximate" => 'Switch',
  344
+	"puzzling_step" => 'Integer',
  345
+	"protein_options" => 'Paragraph',
  346
+	"protein_model" => 'Excl',
  347
+	"dna_options" => 'Paragraph',
  348
+	"ratio" => 'Float',
  349
+	"GTR_options" => 'Paragraph',
  350
+	"GTR_acrate" => 'Float',
  351
+	"GTR_agrate" => 'Float',
  352
+	"GTR_atrate" => 'Float',
  353
+	"GTR_cgrate" => 'Float',
  354
+	"GTR_ctrate" => 'Float',
  355
+	"GTR_gtrate" => 'Float',
  356
+	"nuc_freq" => 'Paragraph',
  357
+	"use_specified" => 'Switch',
  358
+	"a_freq" => 'Float',
  359
+	"c_freq" => 'Float',
  360
+	"g_freq" => 'Float',
  361
+	"dna_model" => 'Excl',
  362
+	"constrain_TN" => 'Switch',
  363
+	"f84_ratio" => 'Float',
  364
+	"y_r" => 'Float',
  365
+	"symmetrize_frequencies" => 'Switch',
  366
+	"rate_options" => 'Paragraph',
  367
+	"rate_heterogeneity" => 'Excl',
  368
+	"alpha" => 'Float',
  369
+	"gamma_number" => 'Integer',
  370
+	"invariable" => 'Float',
  371
+	"user_tree_options" => 'Paragraph',
  372
+	"user_tree" => 'Switch',
  373
+	"tree_file" => 'InFile',
  374
+	"no_tree" => 'Switch',
  375
+	"output_options" => 'Paragraph',
  376
+	"outgroup" => 'Integer',
  377
+	"branch_length" => 'Switch',
  378
+	"estimates" => 'Excl',
  379
+	"estimation_by" => 'Excl',
  380
+	"list_unresolved" => 'Switch',
  381
+	"list_trees" => 'Switch',
  382
+
  383
+    };
  384
+
  385
+    $self->{FORMAT}  = {
  386
+	"Puzzle" => {
  387
+		"perl" => '"Puzzle"',
  388
+	},
  389
+	"stdinput" => {
  390
+		"perl" => '" < params"',
  391
+	},
  392
+	"confirm" => {
  393
+		"perl" => '"y\\n"',
  394
+	},
  395
+	"outfile" => {
  396
+	},
  397
+	"outtree" => {
  398
+	},
  399
+	"outdist" => {
  400
+	},
  401
+	"params" => {
  402
+	},
  403
+	"infile" => {
  404
+		"perl" => '" $infile"',
  405
+	},
  406
+	"seqtype" => {
  407
+		"perl" => '""',
  408
+	},
  409
+	"control_options" => {
  410
+	},
  411
+	"approximate" => {
  412
+		"perl" => '($value)? "" : "v\\n"',
  413
+	},
  414
+	"puzzling_step" => {
  415
+		"perl" => '(defined $value and $value != $vdef)? "n\\n$value\\n" : ""',
  416
+	},
  417
+	"protein_options" => {
  418
+	},
  419
+	"protein_model" => {
  420
+	},
  421
+	"dna_options" => {
  422
+	},
  423
+	"ratio" => {
  424
+		"perl" => '(defined $value) ? "t\\n$value\\n" : ""',
  425
+	},
  426
+	"GTR_options" => {
  427
+	},
  428
+	"GTR_acrate" => {
  429
+		"perl" => '(defined $value and $value != $vdef) ? "1\\n$value\\n" : ""',
  430
+	},
  431
+	"GTR_agrate" => {
  432
+		"perl" => '(defined $value and $value != $vdef) ? "2\\n$value\\n" : ""',
  433
+	},
  434
+	"GTR_atrate" => {
  435
+		"perl" => '(defined $value and $value != $vdef) ? "3\\n$value\\n" : ""',
  436
+	},
  437
+	"GTR_cgrate" => {
  438
+		"perl" => '(defined $value and $value != $vdef) ? "4\\n$value\\n" : ""',
  439
+	},
  440
+	"GTR_ctrate" => {
  441
+		"perl" => '(defined $value and $value != $vdef) ? "5\\n$value\\n" : ""',
  442
+	},
  443
+	"GTR_gtrate" => {
  444
+		"perl" => '(defined $value and $value != $vdef) ? "6\\n$value\\n" : ""',
  445
+	},
  446
+	"nuc_freq" => {
  447
+	},
  448
+	"use_specified" => {
  449
+		"perl" => '($value)? "f\\n" : "" ',
  450
+	},
  451
+	"a_freq" => {
  452
+		"perl" => '"$value\\n"',
  453
+	},
  454
+	"c_freq" => {
  455
+		"perl" => '"$value\\n"',
  456
+	},
  457
+	"g_freq" => {
  458
+		"perl" => '"$value\\n"',
  459
+	},
  460
+	"dna_model" => {
  461
+	},
  462
+	"constrain_TN" => {
  463
+		"perl" => '($value)? "p\\n" : ""',
  464
+	},
  465
+	"f84_ratio" => {
  466
+		"perl" => '(defined $value)? "$value\\n" : ""',
  467
+	},
  468
+	"y_r" => {
  469
+		"perl" => '(defined $value)? "r\\n$value\\n" : ""',
  470
+	},
  471
+	"symmetrize_frequencies" => {
  472
+		"perl" => '($value)? "s\\n" : ""',
  473
+	},
  474
+	"rate_options" => {
  475
+	},
  476
+	"rate_heterogeneity" => {
  477
+	},
  478
+	"alpha" => {
  479
+		"perl" => '(defined $value)? "a\\n$value\\n" : ""',
  480
+	},
  481
+	"gamma_number" => {
  482
+		"perl" => '(defined $value and $value != $vdef)? "c\\n$value\\n" : ""',
  483
+	},
  484
+	"invariable" => {
  485
+		"perl" => '(defined $value)? "i\\n$value\\n" : ""',
  486
+	},
  487
+	"user_tree_options" => {
  488
+	},
  489
+	"user_tree" => {
  490
+		"perl" => '($value)? "k\\n" : "" ',
  491
+	},
  492
+	"tree_file" => {
  493
+		"perl" => '($value)? "$tree_file\\n" : ""',
  494
+	},
  495
+	"no_tree" => {
  496
+		"perl" => '($value)? "k\\nk\\n" : "" ',
  497
+	},
  498
+	"output_options" => {
  499
+	},
  500
+	"outgroup" => {
  501
+		"perl" => '(defined $value)? "o\\n$value\\n" : ""',
  502
+	},
  503
+	"branch_length" => {
  504
+		"perl" => '($value)? "z\\n" : ""',
  505
+	},
  506
+	"estimates" => {
  507
+	},
  508
+	"estimation_by" => {
  509
+	},
  510
+	"list_unresolved" => {
  511
+		"perl" => '($value)? "u\\n" : ""',
  512
+	},
  513
+	"list_trees" => {
  514
+		"perl" => '($value)? "j\\n" : ""',
  515
+	},
  516
+
  517
+    };
  518
+
  519
+    $self->{FILENAMES}  = {
  520
+	"outfile" => '*.puzzle',
  521
+	"outtree" => '*.tree',
  522
+	"outdist" => '*.dist',
  523
+	"params" => 'params',
  524
+
  525
+    };
  526
+
  527
+    $self->{SEQFMT}  = {
  528
+	"infile" => [12],
  529
+
  530
+    };
  531
+
  532
+    $self->{GROUP}  = {
  533
+	"Puzzle" => 0,
  534
+	"stdinput" => 2,
  535
+	"confirm" => 1000,
  536
+	"infile" => 1,
  537
+	"seqtype" => -10,
  538
+	"approximate" => 1,
  539
+	"puzzling_step" => 1,
  540
+	"protein_model" => 1,
  541
+	"ratio" => 1,
  542
+	"GTR_acrate" => 11,
  543
+	"GTR_agrate" => 11,
  544
+	"GTR_atrate" => 11,
  545
+	"GTR_cgrate" => 11,
  546
+	"GTR_ctrate" => 11,
  547
+	"GTR_gtrate" => 11,
  548
+	"use_specified" => 50,
  549
+	"a_freq" => 51,
  550
+	"c_freq" => 52,
  551
+	"g_freq" => 53,
  552
+	"dna_model" => 10,
  553
+	"constrain_TN" => 11,
  554
+	"f84_ratio" => 12,
  555
+	"y_r" => 13,
  556
+	"symmetrize_frequencies" => 11,
  557
+	"rate_heterogeneity" => 20,
  558
+	"alpha" => 21,
  559
+	"gamma_number" => 21,
  560
+	"invariable" => 21,
  561
+	"user_tree" => 1,
  562
+	"tree_file" => 2000,
  563
+	"no_tree" => 1,
  564
+	"outgroup" => 1,
  565
+	"branch_length" => 1,
  566
+	"estimates" => 1,
  567
+	"estimation_by" => 1,
  568
+	"list_unresolved" => 1,
  569
+	"list_trees" => 1,
  570
+
  571
+    };
  572
+
  573
+    $self->{BY_GROUP_PARAMETERS}  = [
  574
+	"seqtype",
  575
+	"nuc_freq",
  576
+	"GTR_options",
  577
+	"outfile",
  578
+	"outtree",
  579
+	"outdist",
  580
+	"params",
  581
+	"dna_options",
  582
+	"Puzzle",
  583
+	"control_options",
  584
+	"protein_options",
  585
+	"rate_options",
  586
+	"user_tree_options",
  587
+	"output_options",
  588
+	"protein_model",
  589
+	"ratio",
  590
+	"infile",
  591
+	"approximate",
  592
+	"user_tree",
  593
+	"no_tree",
  594
+	"puzzling_step",
  595
+	"outgroup",
  596
+	"branch_length",
  597
+	"estimates",
  598
+	"estimation_by",
  599
+	"list_unresolved",
  600
+	"list_trees",
  601
+	"stdinput",
  602
+	"dna_model",
  603
+	"GTR_ctrate",
  604
+	"GTR_gtrate",
  605
+	"GTR_acrate",
  606
+	"constrain_TN",
  607
+	"symmetrize_frequencies",
  608
+	"GTR_agrate",
  609
+	"GTR_atrate",
  610
+	"GTR_cgrate",
  611
+	"f84_ratio",
  612
+	"y_r",
  613
+	"rate_heterogeneity",
  614
+	"gamma_number",
  615
+	"invariable",
  616
+	"alpha",
  617
+	"use_specified",
  618
+	"a_freq",
  619
+	"c_freq",
  620
+	"g_freq",
  621
+	"confirm",
  622
+	"tree_file",
  623
+
  624
+    ];
  625
+
  626
+    $self->{SIZE}  = {
  627
+
  628
+    };
  629
+
  630
+    $self->{ISHIDDEN}  = {
  631
+	"Puzzle" => 1,
  632
+	"stdinput" => 1,
  633
+	"confirm" => 1,
  634
+	"outfile" => 0,
  635
+	"outtree" => 0,
  636
+	"outdist" => 0,
  637
+	"params" => 0,
  638
+	"infile" => 0,
  639
+	"seqtype" => 0,
  640
+	"control_options" => 0,
  641
+	"approximate" => 0,
  642
+	"puzzling_step" => 0,