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comparison pfamScan/Bio/Pfam/HMM/HMM.pm @ 0:68a3648c7d91 draft default tip
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date | Thu, 22 Dec 2016 04:45:31 -0500 |
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1 # HMM.pm | |
2 # | |
3 # Author: finnr | |
4 # Maintainer: $Id: HMM.pm,v 1.1 2009-10-08 12:27:28 jt6 Exp $ | |
5 # Version: $Revision: 1.1 $ | |
6 # Created: Nov 24, 2008 | |
7 # Last Modified: $Date: 2009-10-08 12:27:28 $ | |
8 =head1 NAME | |
9 | |
10 Template - a short description of the class | |
11 | |
12 =cut | |
13 | |
14 package Bio::Pfam::HMM::HMM; | |
15 | |
16 =head1 DESCRIPTION | |
17 | |
18 A more detailed description of what this class does and how it does it. | |
19 | |
20 $Id: HMM.pm,v 1.1 2009-10-08 12:27:28 jt6 Exp $ | |
21 | |
22 =head1 COPYRIGHT | |
23 | |
24 File: HMM.pm | |
25 | |
26 Copyright (c) 2007: Genome Research Ltd. | |
27 | |
28 Authors: Rob Finn (rdf@sanger.ac.uk), John Tate (jt6@sanger.ac.uk) | |
29 | |
30 This is free software; you can redistribute it and/or | |
31 modify it under the terms of the GNU General Public License | |
32 as published by the Free Software Foundation; either version 2 | |
33 of the License, or (at your option) any later version. | |
34 | |
35 This program is distributed in the hope that it will be useful, | |
36 but WITHOUT ANY WARRANTY; without even the implied warranty of | |
37 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
38 GNU General Public License for more details. | |
39 | |
40 You should have received a copy of the GNU General Public License | |
41 along with this program; if not, write to the Free Software | |
42 Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. | |
43 or see the on-line version at http://www.gnu.org/copyleft/gpl.txt | |
44 | |
45 =cut | |
46 | |
47 use strict; | |
48 use warnings; | |
49 | |
50 use Moose; | |
51 use Moose::Util::TypeConstraints; | |
52 use Carp; | |
53 | |
54 #------------------------------------------------------------------------------- | |
55 | |
56 =head1 METHODS | |
57 | |
58 =cut | |
59 | |
60 | |
61 subtype 'hmmVersion' | |
62 => as Str | |
63 => where { $_ =~ m/^HMMER3\/f\s+\[3\.\d+[ab](\d+)?\s+|\s+\[.*\]/ } | |
64 => message { "|$_| does not look like as HMMER3 version" }; | |
65 | |
66 subtype 'hmmName' | |
67 => as Str | |
68 => where { $_ =~ m/\S{1,15}/ } | |
69 => message { "|$_| does not look like Pfam name or SEED" }; | |
70 | |
71 subtype 'hmmAcc' | |
72 => as Str | |
73 => where { $_ =~ m/PF\d{5}/ } | |
74 => message { "|$_| does not look like Pfam accession" }; | |
75 | |
76 | |
77 subtype 'hmmAlpha' | |
78 => as Str | |
79 => where { $_ eq 'amino' or $_ eq 'nucleic' } | |
80 => message { "|$_| does not look like a HMMER3 alphabet" }; | |
81 | |
82 | |
83 subtype 'hmmMsvStats' | |
84 => as HashRef | |
85 => where { defined ($_->{mu}) and defined ($_->{lambda}) and ($_->{lambda} <= 0.8) and ($_->{lambda} >= 0.5) } | |
86 => message { "Mu |$_->{mu}| and lambda |$_->{lambda}| must be defined and lambda must be between 0.5 and 0.8" }; | |
87 | |
88 | |
89 subtype 'hmmViterbiStats' | |
90 => as HashRef | |
91 => where { defined ($_->{mu}) and defined ($_->{lambda}) and ($_->{lambda} <= 0.8) and ($_->{lambda} >= 0.5) } | |
92 => message { "Mu |$_->{mu}| and lambda |$_->{lambda}| must be defined and lambda must be between 0.5 and 0.8" }; | |
93 | |
94 subtype 'hmmForwardStats' | |
95 => as HashRef | |
96 => where { defined ($_->{tau}) and defined ($_->{lambda}) and ($_->{lambda} <= 0.8) and ($_->{lambda} >= 0.5) } | |
97 => message { "Tau |$_->{tau}| and lambda |$_->{lambda}| must be defined and lambda must be between 0.5 and 0.8" }; | |
98 | |
99 has 'version' => ( | |
100 isa => 'hmmVersion', | |
101 is => 'rw', | |
102 required => 1 | |
103 ); | |
104 | |
105 has 'name' => ( | |
106 isa => 'hmmName', | |
107 is => 'rw', | |
108 required => 1 | |
109 ); | |
110 | |
111 has 'accession' => ( | |
112 isa => 'hmmAcc', | |
113 is => 'rw' | |
114 ); | |
115 | |
116 has 'description' => ( | |
117 isa => 'Str', | |
118 is => 'rw' | |
119 ); | |
120 | |
121 has 'length' => ( | |
122 isa => 'Int', | |
123 is => 'rw', | |
124 required => 1 | |
125 ); | |
126 | |
127 has 'alpha' => ( | |
128 isa => 'hmmAlpha', | |
129 is => 'rw', | |
130 required => 1, | |
131 ); | |
132 | |
133 has 'rf' => ( | |
134 isa => 'Bool', | |
135 is => 'rw', | |
136 required => 1 | |
137 ); | |
138 | |
139 has 'mm' => ( | |
140 isa => 'Bool', | |
141 is => 'rw', | |
142 ); | |
143 | |
144 has 'cons' => ( | |
145 isa => 'Bool', | |
146 is => 'rw', | |
147 ); | |
148 | |
149 has 'cs' => ( | |
150 isa => 'Bool', | |
151 is => 'rw', | |
152 required => 1 | |
153 ); | |
154 | |
155 has 'map' => ( | |
156 isa => 'Bool', | |
157 is => 'rw', | |
158 required => 1 | |
159 ); | |
160 | |
161 has 'date' => ( | |
162 isa => 'Str', | |
163 is => 'rw', | |
164 required => 1 | |
165 ); | |
166 | |
167 has 'buildLine' => ( | |
168 isa => 'HashRef[Str]', | |
169 is => 'rw', | |
170 required => 1, | |
171 default => sub { {} }, | |
172 ); | |
173 | |
174 has 'searchMethod' => ( | |
175 isa => 'Str', | |
176 is => 'rw', | |
177 ); | |
178 | |
179 has 'nSeq' => ( | |
180 isa => 'Int', | |
181 is => 'rw', | |
182 required => 1 | |
183 ); | |
184 | |
185 has 'msvStats' => ( | |
186 isa => 'hmmMsvStats', | |
187 is => 'rw', | |
188 required => 1 | |
189 ); | |
190 | |
191 has 'viterbiStats' => ( | |
192 isa => 'hmmViterbiStats', | |
193 is => 'rw', | |
194 required => 1 | |
195 ); | |
196 | |
197 has 'forwardStats' => ( | |
198 isa => 'hmmForwardStats', | |
199 is => 'rw', | |
200 required => 1 | |
201 ); | |
202 | |
203 | |
204 has 'effn' => ( | |
205 isa => 'Num', | |
206 is => 'rw', | |
207 required => 1 | |
208 ); | |
209 | |
210 has 'cksum' => ( | |
211 isa => 'Int', | |
212 is => 'rw', | |
213 required => 1 | |
214 ); | |
215 | |
216 has 'seqGA' => ( | |
217 isa => 'Num', | |
218 is => 'rw', | |
219 ); | |
220 | |
221 has 'domGA' => ( | |
222 isa => 'Num', | |
223 is => 'rw', | |
224 ); | |
225 | |
226 has 'seqTC' => ( | |
227 isa => 'Num', | |
228 is => 'rw', | |
229 ); | |
230 | |
231 has 'domTC' => ( | |
232 isa => 'Num', | |
233 is => 'rw', | |
234 ); | |
235 | |
236 has 'seqNC' => ( | |
237 isa => 'Num', | |
238 is => 'rw', | |
239 ); | |
240 | |
241 has 'domNC' => ( | |
242 isa => 'Num', | |
243 is => 'rw', | |
244 ); | |
245 | |
246 has 'emissionLines' => ( | |
247 isa => 'ArrayRef[ArrayRef]', | |
248 is => 'rw', | |
249 default => sub { [] }, | |
250 ); | |
251 | |
252 has 'mapPos'=> ( | |
253 isa => 'ArrayRef[Int]', | |
254 is => 'rw', | |
255 default => sub{ [] } | |
256 ); | |
257 | |
258 has 'compLines' => ( | |
259 isa => 'ArrayRef[Str]', | |
260 is => 'rw', | |
261 default => sub { [] }, | |
262 ); | |
263 | |
264 __PACKAGE__->meta->make_immutable; | |
265 1; | |
266 |