1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
|
#---------------------------------------------------------
=head1 NAME
Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
=head1 SYNOPSIS
See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers
=head1 DESCRIPTION
Parser for meme.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Stefan Kirov
Email skirov@utk.edu
=head1 APPENDIX
=cut
# Let the code begin...
package Bio::Matrix::PSM::IO::meme;
$Bio::Matrix::PSM::IO::meme::VERSION = '1.7.8';
use Bio::Matrix::PSM::InstanceSite;
use Bio::Matrix::PSM::SiteMatrix;
use Bio::Matrix::PSM::Psm;
use vars qw(@HEADER);
use strict;
use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO);
@Bio::Matrix::PSM::IO::meme::HEADER = qw(e_val sites IC width);
=head2 new
Title : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme',
-file=>$file);
Function: Associates a file with the appropriate parser
Throws : Throws if the file passed is in HTML format or
if the MEME header cannot be found.
Example :
Args : hash
Returns : "Bio::Matrix::PSM::$format"->new(@args);
=cut
sub new {
my($class, @args)=@_;
my $self = $class->SUPER::new(@args);
my ($file)=$self->_rearrange(['FILE'], @args);
my ($query,$tr1)=split(/\./,$file,2);
$self->{file} = $file;
$self->{query}= $query;
$self->{end} = 0;
$self->{_strand}=0; #This we'll need to see if revcom option is used
$self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now
#Skip header
my $line;
while (my $line=$self->_readline) {
$self->throw('Cannot parse HTML, please use text output\n') if ($line=~/<HEAD>/); #Should start parsing HTML output, not a bug deal
chomp($line);
if ($line=~"^ALPHABET") {
$self=_parse_coordinates($self);
last;
}
push @{$self->{unstructured}},$line unless (($line=~/\*{10,}/) || ($line eq ''));
}
$self->_initialize;
return $self;
}
=head2 _parse_coordinates
Title : _parse_coordinates
Usage :
Function:
Throws :
Example : Internal stuff
Returns :
Args :
=cut
sub _parse_coordinates {
my $self=shift;
$self->_readline;
$self->_readline;
my $line=$self->_readline;
while ($line !~ /^\*{10,}/ ) {
chomp $line;
$line =~ s/\s+/,/g;
my ($id1,$w1,$l1,$id2,$w2,$l2)=split(/,/,$line);
push @{$self->{hid}},$id1;
$self->{weight}->{$id1}=$w1;
$self->{length}->{$id1}=$l1;
if ($id2) {
push @{$self->{hid}},$id2;
$self->{weight}->{$id2}=$w2;
$self->{length}->{$id2}=$l2;
}
$line=$self->_readline;
}
return $self;
}
=head2 header
Title : header
Usage : my %header=$psmIO->header;
Function: Returns the header for the MEME file
Throws :
Example : Fetching all the sequences included in the MEME analysis,
being parsed
my %header=$psmIO->header;
foreach my $seqid (@{$header{instances}}) {
my $seq=$db->get_Seq_by_acc($id);
#Do something with the sequence
}
where $db might be Bio::DB:GenBank object, see
Returns : Hash with three keys: instances, weights and lengths, which
should be self-explenatory. Each value is an array
reference. Each array element corresponds to the same
element in the other two arrays. So $header{instances}->[$i]
will refer to the same sequence in the motif file as
$header{weights}->[$i] and $header{lengths}->[$i]
Args : none
Notes : OBSOLETE!
=cut
sub header {
my $self=shift;
my @instances=@{$self->{_inst_name}};
my @weights=@{$self->{_inst_weight}};
my @lengths=@{$self->{_inst_coord}};
return (instances=>\@instances,weights=>\@weights,lengths=>\@lengths);
}
=head2 next_psm
Title : next_psm
Usage : my $psm=$psmIO->next_psm();
Function: Reads the next PSM from the input file, associated with this object
Throws : Throws if the format is inconsistent with the rules for MEME 3.0.4:
no SUMMARY Section present or some keywords are missing/altered.
Example :
Returns : Bio::Matrix::PSM::Psm object
Args : none
=cut
sub next_psm {
#Parses the next prediction and returns a psm objects
my $self=shift;
return if ($self->{end});
my ($endm,$line,$instances,$tr,$width,$motif_id,$sites,$e_val,$id,$ic,$lA,$lC,$lG,$lT);
while (defined( $line = $self->_readline) ) {
#Check if revcom is enabled, not very original check....
$self->{_strand}=1 if (($line=~/^Sequence name/) && ($line=~/Strand/));
if ($line=~ m/\sSite\s/) {
$instances= $self->_parseInstance;
}
#Here starts the next motif
if ( ($line=~/width/) && ($line=~/sites/)) {
chomp($line);
$line=~s/[\t\s=]+/,/g;
$line=~s/\t/,/g;
#Parsing the general information for this prediction
($tr,$motif_id,$tr,$width,$tr,$sites,
$tr,$tr,$tr,$e_val)=split(/,/,$line);
$self->{id}=$self->{query} . $motif_id;
}
if ($line =~ /content/i) {
$line=$self->_readline;
chomp($line);
$line=~s/[\)\(]//g;
($ic)=split(/\s/,$line);
}
#Last info-prob matrix data
if ($line=~/position-specific\s+scoring matrix/) {
($lA,$lC,$lG,$lT)=_parse_logs($self);
}
if ($line=~/^letter-probability\smatrix/) {
my %matrix_dat=$self->_parseMatrix($motif_id);
my $psm= Bio::Matrix::PSM::Psm->new(%matrix_dat,
-instances=>$instances,
-e_val=>$e_val,
-IC=>$ic,
-width=>$width,
-sites=>$sites,
-lA=>$lA,
-lC=>$lC,
-lG=>$lG,
-lT=>$lT,
);
return $psm;
}
if ($line=~"SUMMARY OF MOTIFS") {
$self->{end}=1;
return;
}
$endm=1 if ($line=~/^Time\s/);
}
if ($endm) { #End of file found, end of current motif too, but not all predictions were made as requested (No summary)
$self->{end}=1;
warn "This MEME analysis was terminated prematurely, you may have less motifs than you requested\n";
return;
}
$self->throw("Wrong format\n"); # Multiple keywords not found, probably wrong format
}
=head2 _parseMatrix
Title : _parseMatrix
Usage :
Function: Parses the next site matrix information in the meme file
Throws :
Example : Internal stuff
Returns : hash as for constructing a SiteMatrix object (see SiteMatrixI)
Args : string
=cut
sub _parseMatrix {
my ($self,$id)=@_;
my (@pA,@pC,@pG,@pT);
my $i=0;
my $line = $self->_readline;
#Most important part- the probability matrix
do {
chomp $line;
last if ($line eq '');
$line=~s/^\s+//;
$line=~s/\s+/,/g;
($pA[$i],$pC[$i],$pG[$i],$pT[$i])=split(/,/,$line);
$i++;
$line=$self->_readline;
} until $line =~ /\-{10,}/;
return (-pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,-id=>$id);
}
=head2 _parse_logs
Title : _parse_logs
Usage :
Function: Parses the next site matrix log values in the meme file
Throws :
Example : Internal stuff
Returns : array of array refs
Args : string
=cut
sub _parse_logs {
my $self=shift;
my (@lA,@lC,@lG,@lT);
my $i=0;
$self->_readline; $self->_readline;
my $line = $self->_readline;
#Most important part- the probability matrix
do {
chomp $line;
last if ($line eq '');
$line=~s/^\s+//;
$line=~s/\s+/,/g;
($lA[$i],$lC[$i],$lG[$i],$lT[$i])=split(/,/,$line);
$i++;
$line=$self->_readline;
} until $line =~ /\-{10,}/;
return (\@lA,\@lC,\@lG,\@lT);
}
=head2 _parseInstance
Title : _parseInstance
Usage :
Function: Parses the next sites instances from the meme file
Throws :
Example : Internal stuff
Returns : Bio::Matrix::PSM::InstanceSite object
Args : none
=cut
sub _parseInstance {
my $self = shift;
my $i=0;
$self->_readline;
my ($line,@instance);
while (defined($line=$self->_readline) ) {
last if ($line =~ /\-{5}/ );
chomp($line);
my @comp=split(/\s+/,$line);
my ($id,$start,$score,$strand,$s1,$s2,$s3);
if ( $self->{_strand}) {
($id,$strand,$start,$score,$s1,$s2,$s3)=@comp;
} else {
($id,$start,$score,$s1,$s2,$s3)=@comp;
$strand=1;
}
my $seq= $s1.$s2.$s3;
if ($seq =~ /[^ACGTacgtNnXx\-\.]/) {
my $col=$#comp;
$self->throw("I have not been able to parse the correct instance sequence: $seq, $col columns\n");
}
my $sid = $self->{id} . '@' . $id;
$instance[$i] = Bio::Matrix::PSM::InstanceSite->new
(-mid => $self->{id},
-start => $start,
-score => $score,
-seq => $seq,
-strand => $strand,
-accession_number => $id,
-primary_id => $sid,
-desc => 'Bioperl MEME parser object' );
$i++;
}
$self->{instances} = \@instance;
return \@instance;
}
1;
|
