/usr/share/perl5/Bio/Tools/Run/Meme.pm is in libbio-perl-run-perl 1.7.1-3.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 | # BioPerl module for Meme
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Meme - Wrapper for Meme Program
=head1 SYNOPSIS
use Bio::Tools::Run::Meme;
my $factory = Bio::Tools::Run::Meme->new(-dna => 1, -mod => 'zoops');
# return a Bio::AlignIO given Bio::PrimarySeqI objects
my $alignio = $factory->run($seq1, $seq2, $seq3...);
# add a Bio::Map::Prediction to the appropriate maps given Bio::Map::GeneMap
# objects (predict on the full map sequences supplied) or Bio::Map::Gene
# objects (predict on the full map sequences of the maps the supplied Genes
# are on) or Bio::Map::PositionWithSequence objects
my $prediction = $factory->run($biomap1, $biomap2, $biomap3...);
=head1 DESCRIPTION
This is a wrapper for running meme, a transcription factor binding site
prediction program. It can be found here:
http://meme.sdsc.edu/meme4/meme-download.html
You can try supplying normal meme command-line arguments to new(), eg.
new(-mod => 'oops') or calling arg-named methods (excluding the initial
hyphen(s), eg. $factory->mod('oops') to set the -mod option to 'oops').
You will need to enable this MEME wrapper to find the meme program. During
standard installation of meme you will have set up an environment variable
called MEME_BIN which is used for this purpose.
=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:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
package Bio::Tools::Run::Meme;
use strict;
use Bio::SeqIO;
use Bio::AlignIO;
use Bio::Map::Prediction;
use Bio::Map::Position;
use base qw(Bio::Tools::Run::WrapperBase);
our $PROGRAM_NAME = 'meme';
our $PROGRAM_DIR = $ENV{'MEME_BIN'};
# methods for the meme args we support
our @PARAMS = qw(mod nmotifs evt nsites minsites maxsites wnsites w minw maxw
wg ws bfile maxiter distance prior b plib spfuzz spmap cons
maxsize p time sf);
our @SWITCHES = qw(dna protein nomatrim noendgaps revcomp pal);
# just to be explicit, args we don't support (yet) or we handle ourselves
our @UNSUPPORTED = qw(h text nostatus);
=head2 new
Title : new
Usage : $rm->new($seq)
Function: creates a new wrapper
Returns: Bio::Tools::Run::Meme
Args : Most options understood by meme can be supplied as key =>
value pairs, with a boolean value for switches. -quiet can also be
set to silence meme completely.
These options can NOT be used with this wrapper (they are handled
internally or don't make sense in this context):
-h -text -nostatus
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->_set_from_args(\@args, -methods => [@PARAMS, @SWITCHES, 'quiet'],
-create => 1);
return $self;
}
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return $PROGRAM_NAME;
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return $PROGRAM_DIR;
}
=head2 version
Title : version
Usage : n/a
Function: Determine the version number of the program, which is
non-discoverable for Meme
Returns : undef
Args : none
=cut
sub version {
return;
}
=head2 run
Title : run
Usage : $rm->run($seq1, $seq2, $seq3...);
Function: Run Meme on the sequences/Bio::Map::* set as the argument
Returns : Bio::AlignIO if sequence objects supplied, OR
Bio::Map::Prediction if Bio::Map::* objects supplied
undef if no executable found
Args : list of Bio::PrimarySeqI compliant objects, OR
list of Bio::Map::GeneMap objects, OR
list of Bio::Map::Gene objects, OR
list of Bio::Map::PositionWithSequence objects
=cut
sub run {
my ($self, @things) = @_;
my $infile = $self->_setinput(@things);
return $self->_run($infile);
}
=head2 _run
Title : _run
Usage : $rm->_run ($filename,$param_string)
Function: internal function that runs meme
Returns : as per run(), undef if no executable found
Args : the filename to the input sequence file
=cut
sub _run {
my ($self, $infile) = @_;
my $exe = $self->executable || return;
my $outfile = $infile.".out";
my $command = $exe.$self->_setparams($infile, $outfile);
$self->debug("meme command = $command\n");
open(my $pipe, "$command |") || $self->throw("meme call ($command) failed to start: $? | $!");
my $error = '';
while (<$pipe>) {
print unless $self->quiet;
$error .= $_;
}
close($pipe) || ($error ? $self->throw("meme call ($command) failed: $error") : $self->throw("meme call ($command) crashed: $?"));
#my $status = system($cmd_str);
#$self->throw("Meme call ($cmd_str) crashed: $?\n") unless $status == 0;
my $aio = Bio::AlignIO->new(-format => 'meme', -file => $outfile);
unless ($self->{map_mode}) {
# return directly the AlignIO
return $aio;
}
else {
# use the AlignIO meme parser to generate a Bio::Map::Prediction and
# return that
my $pred = Bio::Map::Prediction->new(-source => "meme");
while (my $aln = $aio->next_aln) {
foreach my $seq ($aln->each_seq) {
my $id = $seq->id;
unless ($id) {
$self->warn("Got a sequence in the alignment with no id, but I need one to determine the map");
next;
}
my ($uid) = $id =~ /^([^\[]+)/;
my $map = Bio::Map::GeneMap->get(-uid => $uid);
my ($start, $end) = ($seq->start, $seq->end);
if ($seq->strand == -1) {
my $length;
my ($pos_s, $pos_e) = $id =~ /\[(\d+)\.\.(\d+)\]$/;
if (defined($pos_s) && defined($pos_e)) {
$length = $pos_e - $pos_s + 1;
}
else {
$length = length($map->seq);
}
my $motif_length = $end - $start + 1;
$end = $length - $start + 1;
$start = $end - $motif_length + 1;
}
Bio::Map::Position->new(-element => $pred,
-start => $start,
-end => $end,
-map => $map);
}
}
delete $self->{map_mode};
return $pred;
}
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for meme program
Returns : parameter string to be passed to meme
Args : none
=cut
sub _setparams {
my ($self, $infile, $outfile) = @_;
my $param_string = ' '.$infile;
# -text and -nostatus must be set
$param_string .= ' -text -nostatus';
$param_string .= $self->SUPER::_setparams(-params => \@PARAMS,
-switches => \@SWITCHES,
-dash => 1);
$param_string .= " > $outfile";
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$param_string .= " 2> $null" if $self->quiet || $self->verbose < 0;
return $param_string;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: writes input sequence to file and return the file name
Returns : string (file name)
Args : as per run()
=cut
sub _setinput {
my ($self, @inputs) = @_;
$self->throw("At least two sequence or map objects must be supplied") unless @inputs >= 2;
ref($inputs[0]) || $self->throw("Inputs must be object references");
my ($fh, $outfile) = $self->io->tempfile(-dir => $self->tempdir);
my $out = Bio::SeqIO->new(-fh => $fh, '-format' => 'fasta');
my %done;
foreach my $input (@inputs) {
if ($input->isa('Bio::Map::MappableI')) {
# we want to work on all its maps, since mappables themselves don't
# have sequences
push(@inputs, $input->known_maps);
next;
}
$input->can('seq') || $self->throw("Supplied an input [$input] with no seq() method!");
if ($input->isa('Bio::Map::EntityI')) {
$self->{map_mode} = 1;
if ($input->isa('Bio::Map::MapI')) {
# change the id of the seq so we'll know what input object it
# came from later
my $id = $input->unique_id;
next if $done{$id};
$input->id($id);
$done{$id} = 1;
#*** should this be automatic in GeneMap? Anyway, we don't want
# to alter users genemap id here permanently...
}
else {
my $id = $input->id;
unless ($id) {
$input->id($input->map->unique_id.'['.$input->toString.']');
}
}
}
$out->write_seq($input);
}
close($fh);
return $outfile;
}
=head1 Bio::Tools::Run::Wrapper methods
=cut
=head2 no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
=cut
=head2 save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
=cut
=head2 outfile_name
Title : outfile_name
Usage : my $outfile = $codeml->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
=cut
=head2 tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
=cut
=head2 cleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
=cut
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
=cut
1;
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