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comparison pfamScan/Bio/Pfam/HMM/HMMIO.pm @ 0:68a3648c7d91 draft default tip
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author | matteoc |
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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: HMMIO.pm,v 1.3 2010-01-12 17:00:26 jm14 Exp $ | |
5 # Version: $Revision: 1.3 $ | |
6 # Created: Nov 24, 2008 | |
7 # Last Modified: $Date: 2010-01-12 17:00:26 $ | |
8 =head1 NAME | |
9 | |
10 Template - a short description of the class | |
11 | |
12 =cut | |
13 | |
14 package Bio::Pfam::HMM::HMMIO; | |
15 | |
16 =head1 DESCRIPTION | |
17 | |
18 A more detailed description of what this class does and how it does it. | |
19 | |
20 $Id: HMMIO.pm,v 1.3 2010-01-12 17:00:26 jm14 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 use Bio::Pfam::HMM::HMM; | |
54 | |
55 #------------------------------------------------------------------------------- | |
56 | |
57 =head1 METHODS | |
58 | |
59 =cut | |
60 sub readHMM { | |
61 my ($this, $hmm) = @_; | |
62 | |
63 unless($hmm){ | |
64 confess("No HMM passed in!"); | |
65 } | |
66 chomp($hmm); | |
67 | |
68 my @input; | |
69 if(ref($hmm) eq 'GLOB'){ | |
70 @input = <$hmm>; | |
71 }elsif($hmm !~ /\n/ and -e $hmm and -s $hmm){ | |
72 #Assume that we have a filename and try and open it; | |
73 open(HMM, $hmm) || confess("Could not open $hmm:[$!]"); | |
74 @input = <HMM>; | |
75 }else{ | |
76 @input = split(/\n/, $hmm); | |
77 } | |
78 | |
79 | |
80 | |
81 #Parse the header section! | |
82 #HMMER3/f [3.1b1 | May 2013] | |
83 #NAME SEED | |
84 #ACC PF000001.1 | |
85 #DESC A description | |
86 #LENG 55 | |
87 #ALPH amino | |
88 #RF no | |
89 #MM no | |
90 #CONS yes | |
91 #CS no | |
92 #MAP yes | |
93 #DATE Fri Nov 21 09:58:16 2008 | |
94 #COM [1] /Users/finnr/Work/Software/hmmer-3.0.20081101/bin/hmmbuild -o hmmbuild.log HMM SEED | |
95 #NSEQ 279 | |
96 #EFFN 4.966292 | |
97 #STATS LOCAL MSV -11.4716 0.69948 | |
98 #STATS LOCAL VITERBI -12.3713 0.69948 | |
99 #STATS LOCAL FORWARD -5.5807 0.69948 | |
100 | |
101 #To add GA, TC, NC, CKSUM, DESC | |
102 my($objHash); | |
103 my $i =0; | |
104 foreach ( @input ){ | |
105 if(my ($version) = $_ =~ /(HMMER3.*)/){ | |
106 $objHash->{version} = $version; | |
107 }elsif(my ($acc) = $_ =~ /^ACC\s+(PF\d+\.\d+)$/){ | |
108 $objHash->{accession} = $acc; | |
109 }elsif(/NAME\s+(\S+)/){ | |
110 $objHash->{name} = $1 ; | |
111 }elsif(/DESC\s+(.*)/){ | |
112 $objHash->{description} = $1 ; | |
113 }elsif(my ($length) = $_ =~ /^LENG\s+(\d+)/){ | |
114 $objHash->{length} = $length; | |
115 }elsif( my ($alpha) = $_ =~ /^ALPH\s+(\S+)/){ | |
116 $objHash->{alpha} = $alpha; | |
117 }elsif( my ($rf) = $_ =~ /^RF\s+(no|yes)/){ | |
118 $objHash->{rf} = ($rf eq "no") ? 0 : 1; | |
119 }elsif( my ($mm) = $_ =~ /^MM\s+(no|yes)/){ | |
120 $objHash->{mm} = ($mm eq "no") ? 0 : 1; | |
121 }elsif( my ($cons) = $_ =~ /^CONS\s+(no|yes)/){ | |
122 $objHash->{cons} = ($cons eq "no") ? 0 : 1; | |
123 }elsif(my ($cs) = $_ =~ /^CS\s+(no|yes)/ ){ | |
124 $objHash->{cs} = ($cs eq "no") ? 0 : 1; | |
125 }elsif(my ($map) = $_ =~ /^MAP\s+(no|yes)/){ | |
126 $objHash->{map} = ($map eq "no") ? 0 : 1; | |
127 }elsif(my ($date) = $_ =~ /^DATE\s+(.*)/){ | |
128 $objHash->{date} = $date; | |
129 }elsif(my ($sm) = $_ =~ /^SM\s+(.*)/){ | |
130 $objHash->{searchMethod} = $sm; | |
131 | |
132 }elsif(my ($options, $hmmName, $alignName) = $input[$i] =~ /^BM.*hmmbuild(.*)? (\S+) (\S+)$/){ | |
133 $objHash->{buildLine} = { cmd => 'hmmbuild', | |
134 options => $options, | |
135 name => $hmmName, | |
136 align => $alignName } ; | |
137 }elsif(my($noSeqs) = $_ =~ /^NSEQ\s+(\d+)/){ | |
138 $objHash->{nSeq} = $noSeqs; | |
139 }elsif( my($effn) = $_ =~ /^EFFN\s+(\d+\.\d+)/){ | |
140 #EFFN 4.966292 | |
141 $objHash->{effn} = $effn ; | |
142 }elsif( my ( $cksum ) = $_ =~ /^CKSUM (\d+)/){ | |
143 $objHash->{cksum} = $cksum ; | |
144 }elsif(/GA\s+(\S+)\s+(\S+)\;/){ | |
145 $objHash->{seqGA} = $1; | |
146 $objHash->{domGA} = $2; | |
147 }elsif(/TC\s+(\S+)\s+(\S+)\;/){ | |
148 $objHash->{seqTC} = $1; | |
149 $objHash->{domTC} = $2; | |
150 }elsif(/NC\s+(\S+)\s+(\S+)\;/){ | |
151 $objHash->{seqNC} = $1; | |
152 $objHash->{domNC} = $2; | |
153 }elsif( my ($msv_mu, $msv_lambda ) = $_ =~ /^STATS LOCAL MSV\s+(\S+)\s+(0\.\d+)/){ | |
154 $objHash->{msvStats} = { mu => $msv_mu, lambda => $msv_lambda}; | |
155 }elsif( my ($viterbi_mu, $viterbi_lambda ) = $_ =~ /^STATS LOCAL VITERBI\s+(\S+)\s+(0\.\d+)/){ | |
156 $objHash->{viterbiStats} = { mu => $viterbi_mu, lambda => $viterbi_lambda }; | |
157 }elsif( my ($forward_tau, $forward_lambda ) = $_ =~ /^STATS LOCAL FORWARD\s+(\S+)\s+(0\.\d+)/){ | |
158 $objHash->{forwardStats} = {tau => $forward_tau, lambda => $forward_lambda}; | |
159 }elsif( $_ =~ /^HMM\s+A/){ | |
160 last; | |
161 }else{ | |
162 confess("Got a bad HMM header line:$input[$i]\n"); | |
163 } | |
164 $i++; | |
165 } | |
166 | |
167 my $hmmObj = Bio::Pfam::HMM::HMM->new($objHash); | |
168 | |
169 | |
170 #The next two lines are stand lines | |
171 #HMM A C D E F G H I K L M N P Q R S T V W Y | |
172 # m->m m->i m->d i->m i->i d->m d->d | |
173 $i++; | |
174 | |
175 | |
176 #Add the comp line | |
177 for( my $line = 0; $line <=2; $line++){ | |
178 $i++; | |
179 my @l = split(/\s+/, $input[$i]); | |
180 my @c; | |
181 if($line == 0 ){ | |
182 @c = @l[2..21]; | |
183 }elsif( $line == 1){ | |
184 @c = @l[1..20]; | |
185 }elsif($line == 2){ | |
186 @c = @l[1..7]; | |
187 } | |
188 $hmmObj->compLines->[$line] = \@c; | |
189 } | |
190 | |
191 | |
192 | |
193 for(my $pos = 0; $pos < $hmmObj->length; $pos++){ | |
194 #There are three lines per position - match emission line, insert emission line, state transition line | |
195 for( my $line = 0; $line <=2; $line++){ | |
196 $i++; | |
197 my @l = split(/\s+/, $input[$i]); | |
198 my @e; | |
199 if($line == 0 ){ | |
200 @e = @l[2..21]; | |
201 if($hmmObj->map){ | |
202 $hmmObj->mapPos->[$pos] = $l[22]; | |
203 } | |
204 }elsif( $line == 1){ | |
205 @e = @l[1..20]; | |
206 }elsif($line == 2){ | |
207 @e = @l[1..7]; | |
208 } | |
209 $hmmObj->emissionLines->[$pos]->[$line] = \@e; | |
210 } | |
211 } | |
212 | |
213 if($input[$i++] =~ /^\/\/$/){ | |
214 confess("Expected file terminator //, but got $input[$i]\n"); | |
215 } | |
216 | |
217 #No veryifiy that we have COMP line and the the number of emissionlines is equivalent to length | |
218 unless(scalar( @{ $hmmObj->emissionLines } ) == $hmmObj->length){ | |
219 confess("Number of emssionLines does not match the length of the model, got ".scalar( @{ $hmmObj->emissionLines} ). | |
220 " expected ".$hmmObj->length); | |
221 } | |
222 | |
223 unless($hmmObj->compLines){ | |
224 confess("No compLine set on HMM"); | |
225 } | |
226 | |
227 if($hmmObj->map){ | |
228 unless(scalar(@{$hmmObj->mapPos}) == $hmmObj->length ){ | |
229 confess("HMM object had map set, but the number of map positions does not match the length of the HMM"); | |
230 }; | |
231 } | |
232 return $hmmObj; | |
233 } | |
234 | |
235 | |
236 | |
237 sub writeHMM { | |
238 my ($this, $hmm, $hmmObj) = @_; | |
239 | |
240 unless($hmm){ | |
241 confess("No HMM out file passed in!"); | |
242 } | |
243 | |
244 unless(ref($hmm) eq 'GLOB'){ | |
245 my $hmmFile = $hmm; | |
246 $hmm = undef; | |
247 #Assume that we have a filename and try and open it; | |
248 open($hmm, ">$hmmFile") || confess("Could not open $hmmFile:[$!]"); | |
249 } | |
250 | |
251 print $hmm $hmmObj->version."\n"; | |
252 printf $hmm ("%-5s %s\n", "NAME", $hmmObj->name); | |
253 printf $hmm ("%-5s %s\n", "ACC", $hmmObj->accession) if($hmmObj->accession); | |
254 printf $hmm ("%-5s %s\n", "DESC", $hmmObj->description) if($hmmObj->description); | |
255 printf $hmm ("%-5s %d\n", "LENG", $hmmObj->length); | |
256 printf $hmm ("%-5s %s\n", "ALPH", $hmmObj->alpha); | |
257 printf $hmm ("%-5s %s\n", "RF", ($hmmObj->rf ? "yes" : "no")); | |
258 printf $hmm ("%-5s %s\n", "MM", ($hmmObj->mm ? "yes" : "no")); | |
259 printf $hmm ("%-5s %s\n", "CONS", ($hmmObj->cons ? "yes" : "no")); | |
260 printf $hmm ("%-5s %s\n", "CS", ($hmmObj->cs ? "yes" : "no")); | |
261 printf $hmm ("%-5s %s\n", "MAP", ($hmmObj->map ? "yes" : "no")); | |
262 printf $hmm ("%-5s %s\n", "DATE", $hmmObj->date); | |
263 printf $hmm ("%-5s %d\n", "NSEQ", $hmmObj->nSeq); | |
264 printf $hmm ("%-5s %f\n", "EFFN", $hmmObj->effn); | |
265 printf $hmm ("%-5s %d\n", "CKSUM", $hmmObj->cksum); | |
266 printf $hmm ("%-5s %.2f %.2f;\n", "GA", $hmmObj->seqGA, $hmmObj->domGA) if(defined($hmmObj->seqGA)); | |
267 printf $hmm ("%-5s %.2f %.2f;\n", "TC", $hmmObj->seqTC, $hmmObj->domTC) if(defined($hmmObj->seqTC)); | |
268 printf $hmm ("%-5s %.2f %.2f;\n", "NC", $hmmObj->seqNC, $hmmObj->domNC) if(defined($hmmObj->seqNC)); | |
269 | |
270 printf $hmm ("%-5s %s %-9s %.4f %.5f\n", "STATS", "LOCAL", "MSV", $hmmObj->msvStats->{mu}, $hmmObj->msvStats->{lambda}); | |
271 printf $hmm ("%-5s %s %-9s %.4f %.5f\n", "STATS", "LOCAL", "VITERBI", $hmmObj->viterbiStats->{mu}, $hmmObj->viterbiStats->{lambda}); | |
272 printf $hmm ("%-5s %s %-9s %.4f %.5f\n", "STATS", "LOCAL", "FORWARD", $hmmObj->forwardStats->{tau}, $hmmObj->forwardStats->{lambda}); | |
273 | |
274 print $hmm <<EOF; | |
275 HMM A C D E F G H I K L M N P Q R S T V W Y | |
276 m->m m->i m->d i->m i->i d->m d->d | |
277 EOF | |
278 | |
279 printf $hmm ("%7s ", "COMPO"); | |
280 foreach my $s (@{$hmmObj->compLines->[0]}){ | |
281 printf $hmm (" %7s", $s); | |
282 } | |
283 print $hmm "\n"; | |
284 | |
285 print $hmm (" " x 8); | |
286 foreach my $s (@{$hmmObj->compLines->[1]}){ | |
287 printf $hmm (" %7s", $s); | |
288 } | |
289 print $hmm "\n"; | |
290 | |
291 print $hmm (" " x 8); | |
292 foreach my $s (@{$hmmObj->compLines->[2]}){ | |
293 printf $hmm (" %7s", $s); | |
294 } | |
295 print $hmm "\n"; | |
296 | |
297 | |
298 my $pos = 1; | |
299 foreach my $el (@{ $hmmObj->emissionLines }){ | |
300 printf $hmm ("%7s ", $pos); | |
301 foreach my $s (@{$el->[0]}){ | |
302 printf $hmm (" %7s", $s); | |
303 } | |
304 if($hmmObj->map){ | |
305 printf $hmm ("%7s - -\n", $hmmObj->mapPos->[$pos - 1]); | |
306 }else{ | |
307 print $hmm "\n"; | |
308 } | |
309 print $hmm (" " x 8); | |
310 foreach my $s (@{$el->[1]}){ | |
311 printf $hmm (" %7s", $s); | |
312 } | |
313 print $hmm "\n"; | |
314 print $hmm (" " x 8); | |
315 foreach my $s (@{$el->[2]}){ | |
316 printf $hmm (" %7s", $s); | |
317 } | |
318 print $hmm "\n"; | |
319 $pos++; | |
320 } | |
321 | |
322 | |
323 print $hmm "//\n"; | |
324 } | |
325 | |
326 | |
327 | |
328 1; | |
329 |