| Filename | /Users/ap13/perl5/lib/perl5/Bio/Tools/GFF.pm |
| Statements | Executed 18 statements in 4.66ms |
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| 1 | 1 | 1 | 2.87ms | 16.6ms | Bio::Tools::GFF::BEGIN@152 |
| 1 | 1 | 1 | 2.28ms | 31.9ms | Bio::Tools::GFF::BEGIN@151 |
| 1 | 1 | 1 | 389µs | 37.5ms | Bio::Tools::GFF::BEGIN@150 |
| 1 | 1 | 1 | 29µs | 78µs | Bio::Tools::GFF::BEGIN@147 |
| 1 | 1 | 1 | 17µs | 46µs | Bio::Tools::GFF::BEGIN@148 |
| 1 | 1 | 1 | 12µs | 601µs | Bio::Tools::GFF::BEGIN@154 |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::DESTROY |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::PRINT |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::READLINE |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::TIEHANDLE |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::_feature_idx_by_seq_id |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::_from_gff1_string |
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| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::_incrementGFF3ID |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::_parse_header |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::_parse_sequence |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::_seq_by_id_h |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::features_attached_to_seqs |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::fh |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::from_gff_string |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::get_seqs |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::gff_string |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::gff_version |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::ignore_sequence |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::new |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::newFh |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::next_feature |
| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::next_segment |
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| 0 | 0 | 0 | 0s | 0s | Bio::Tools::GFF::write_feature |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::Tools::GFF | ||||
| 3 | # | ||||
| 4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
| 5 | # | ||||
| 6 | # Cared for by the Bioperl core team | ||||
| 7 | # | ||||
| 8 | # Copyright Matthew Pocock | ||||
| 9 | # | ||||
| 10 | # You may distribute this module under the same terms as perl itself | ||||
| 11 | |||||
| 12 | # POD documentation - main docs before the code | ||||
| 13 | |||||
| 14 | =head1 NAME | ||||
| 15 | |||||
| 16 | Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser | ||||
| 17 | |||||
| 18 | =head1 SYNOPSIS | ||||
| 19 | |||||
| 20 | use Bio::Tools::GFF; | ||||
| 21 | |||||
| 22 | # specify input via -fh or -file | ||||
| 23 | my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2); | ||||
| 24 | my $feature; | ||||
| 25 | # loop over the input stream | ||||
| 26 | while($feature = $gffio->next_feature()) { | ||||
| 27 | # do something with feature | ||||
| 28 | } | ||||
| 29 | $gffio->close(); | ||||
| 30 | |||||
| 31 | # you can also obtain a GFF parser as a SeqAnalasisParserI in | ||||
| 32 | # HT analysis pipelines (see Bio::SeqAnalysisParserI and | ||||
| 33 | # Bio::Factory::SeqAnalysisParserFactory) | ||||
| 34 | my $factory = Bio::Factory::SeqAnalysisParserFactory->new(); | ||||
| 35 | my $parser = $factory->get_parser(-input => \*STDIN, -method => "gff"); | ||||
| 36 | while($feature = $parser->next_feature()) { | ||||
| 37 | # do something with feature | ||||
| 38 | } | ||||
| 39 | |||||
| 40 | =head1 DESCRIPTION | ||||
| 41 | |||||
| 42 | This class provides a simple GFF parser and writer. In the sense of a | ||||
| 43 | SeqAnalysisParser, it parses an input file or stream into SeqFeatureI | ||||
| 44 | objects, but is not in any way specific to a particular analysis | ||||
| 45 | program and the output that program produces. | ||||
| 46 | |||||
| 47 | That is, if you can get your analysis program spit out GFF, here is | ||||
| 48 | your result parser. | ||||
| 49 | |||||
| 50 | =head1 GFF3 AND SEQUENCE DATA | ||||
| 51 | |||||
| 52 | GFF3 supports sequence data; see | ||||
| 53 | |||||
| 54 | http://www.sequenceontology.org/gff3.shtml | ||||
| 55 | |||||
| 56 | There are a number of ways to deal with this - | ||||
| 57 | |||||
| 58 | If you call | ||||
| 59 | |||||
| 60 | $gffio->ignore_sequence(1) | ||||
| 61 | |||||
| 62 | prior to parsing the sequence data is ignored; this is useful if you | ||||
| 63 | just want the features. It avoids the memory overhead in building and | ||||
| 64 | caching sequences | ||||
| 65 | |||||
| 66 | Alternatively, you can call either | ||||
| 67 | |||||
| 68 | $gffio->get_seqs() | ||||
| 69 | |||||
| 70 | Or | ||||
| 71 | |||||
| 72 | $gffio->seq_id_by_h() | ||||
| 73 | |||||
| 74 | At the B<end> of parsing to get either a list or hashref of Bio::Seq | ||||
| 75 | objects (see the documentation for each of these methods) | ||||
| 76 | |||||
| 77 | Note that these objects will not have the features attached - you have | ||||
| 78 | to do this yourself, OR call | ||||
| 79 | |||||
| 80 | $gffio->features_attached_to_seqs(1) | ||||
| 81 | |||||
| 82 | PRIOR to parsing; this will ensure that the Seqs have the features | ||||
| 83 | attached; ie you will then be able to call | ||||
| 84 | |||||
| 85 | $seq->get_SeqFeatures(); | ||||
| 86 | |||||
| 87 | And use Bio::SeqIO methods | ||||
| 88 | |||||
| 89 | Note that auto-attaching the features to seqs will incur a higher | ||||
| 90 | memory overhead as the features must be cached until the sequence data | ||||
| 91 | is found | ||||
| 92 | |||||
| 93 | =head1 TODO | ||||
| 94 | |||||
| 95 | Make a Bio::SeqIO class specifically for GFF3 with sequence data | ||||
| 96 | |||||
| 97 | =head1 FEEDBACK | ||||
| 98 | |||||
| 99 | =head2 Mailing Lists | ||||
| 100 | |||||
| 101 | User feedback is an integral part of the evolution of this and other | ||||
| 102 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
| 103 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
| 104 | |||||
| 105 | bioperl-l@bioperl.org - General discussion | ||||
| 106 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
| 107 | |||||
| 108 | =head2 Support | ||||
| 109 | |||||
| 110 | Please direct usage questions or support issues to the mailing list: | ||||
| 111 | |||||
| 112 | I<bioperl-l@bioperl.org> | ||||
| 113 | |||||
| 114 | rather than to the module maintainer directly. Many experienced and | ||||
| 115 | reponsive experts will be able look at the problem and quickly | ||||
| 116 | address it. Please include a thorough description of the problem | ||||
| 117 | with code and data examples if at all possible. | ||||
| 118 | |||||
| 119 | =head2 Reporting Bugs | ||||
| 120 | |||||
| 121 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 122 | the bugs and their resolution. Bug reports can be submitted the web: | ||||
| 123 | |||||
| 124 | https://github.com/bioperl/bioperl-live/issues | ||||
| 125 | |||||
| 126 | =head1 AUTHOR - Matthew Pocock | ||||
| 127 | |||||
| 128 | Email mrp-at-sanger.ac.uk | ||||
| 129 | |||||
| 130 | =head1 CONTRIBUTORS | ||||
| 131 | |||||
| 132 | Jason Stajich, jason-at-biperl-dot-org | ||||
| 133 | Chris Mungall, cjm-at-fruitfly-dot-org | ||||
| 134 | Steffen Grossmann [SG], grossman at molgen.mpg.de | ||||
| 135 | Malcolm Cook, mec-at-stowers-institute.org | ||||
| 136 | |||||
| 137 | =head1 APPENDIX | ||||
| 138 | |||||
| 139 | The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ | ||||
| 140 | |||||
| 141 | =cut | ||||
| 142 | |||||
| 143 | # Let the code begin... | ||||
| 144 | |||||
| 145 | package Bio::Tools::GFF; | ||||
| 146 | |||||
| 147 | 2 | 56µs | 2 | 127µs | # spent 78µs (29+49) within Bio::Tools::GFF::BEGIN@147 which was called:
# once (29µs+49µs) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 147 # spent 78µs making 1 call to Bio::Tools::GFF::BEGIN@147
# spent 49µs making 1 call to vars::import |
| 148 | 2 | 44µs | 2 | 75µs | # spent 46µs (17+29) within Bio::Tools::GFF::BEGIN@148 which was called:
# once (17µs+29µs) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 148 # spent 46µs making 1 call to Bio::Tools::GFF::BEGIN@148
# spent 29µs making 1 call to strict::import |
| 149 | |||||
| 150 | 2 | 180µs | 1 | 37.5ms | # spent 37.5ms (389µs+37.1) within Bio::Tools::GFF::BEGIN@150 which was called:
# once (389µs+37.1ms) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 150 # spent 37.5ms making 1 call to Bio::Tools::GFF::BEGIN@150 |
| 151 | 2 | 147µs | 1 | 31.9ms | # spent 31.9ms (2.28+29.6) within Bio::Tools::GFF::BEGIN@151 which was called:
# once (2.28ms+29.6ms) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 151 # spent 31.9ms making 1 call to Bio::Tools::GFF::BEGIN@151 |
| 152 | 2 | 202µs | 1 | 16.6ms | # spent 16.6ms (2.87+13.7) within Bio::Tools::GFF::BEGIN@152 which was called:
# once (2.87ms+13.7ms) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 152 # spent 16.6ms making 1 call to Bio::Tools::GFF::BEGIN@152 |
| 153 | |||||
| 154 | 2 | 4.01ms | 2 | 1.19ms | # spent 601µs (12+589) within Bio::Tools::GFF::BEGIN@154 which was called:
# once (12µs+589µs) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 154 # spent 601µs making 1 call to Bio::Tools::GFF::BEGIN@154
# spent 589µs making 1 call to base::import |
| 155 | |||||
| 156 | 1 | 500ns | my $i = 0; | ||
| 157 | 1 | 6µs | my %GFF3_ID_Tags = map { $_ => $i++ } qw(ID Parent Target); | ||
| 158 | |||||
| 159 | # for skipping data that may be represented elsewhere; currently, this is | ||||
| 160 | # only the score | ||||
| 161 | 1 | 1µs | my %SKIPPED_TAGS = map { $_ => 1 } qw(score); | ||
| 162 | |||||
| 163 | |||||
| 164 | =head2 new | ||||
| 165 | |||||
| 166 | Title : new | ||||
| 167 | Usage : my $parser = Bio::Tools::GFF->new(-gff_version => 2, | ||||
| 168 | -file => "filename.gff"); | ||||
| 169 | or | ||||
| 170 | my $writer = Bio::Tools::GFF->new(-gff_version => 3, | ||||
| 171 | -file => ">filename.gff3"); | ||||
| 172 | Function: Creates a new instance. Recognized named parameters are -file, -fh, | ||||
| 173 | and -gff_version. | ||||
| 174 | Returns : a new object | ||||
| 175 | Args : named parameters | ||||
| 176 | -gff_version => [1,2,3] | ||||
| 177 | |||||
| 178 | =cut | ||||
| 179 | |||||
| 180 | { # make a class variable such that we can generate unique ID's over | ||||
| 181 | # a session, no matter how many instances of GFF.pm we make | ||||
| 182 | # since these have to be unique within the scope of a GFF file. | ||||
| 183 | |||||
| 184 | 2 | 800ns | my $gff3_featureID = 0; | ||
| 185 | |||||
| 186 | sub _incrementGFF3ID { | ||||
| 187 | my ($self) = @_; | ||||
| 188 | return ++ $gff3_featureID; | ||||
| 189 | } | ||||
| 190 | } | ||||
| 191 | |||||
| 192 | |||||
| 193 | sub new { | ||||
| 194 | my ($class, @args) = @_; | ||||
| 195 | my $self = $class->SUPER::new(@args); | ||||
| 196 | |||||
| 197 | my ($gff_version, $noparse) = $self->_rearrange([qw(GFF_VERSION NOPARSE)],@args); | ||||
| 198 | |||||
| 199 | # initialize IO | ||||
| 200 | $self->_initialize_io(@args); | ||||
| 201 | $self->_parse_header() unless $noparse; | ||||
| 202 | |||||
| 203 | $gff_version ||= 2; | ||||
| 204 | if( ! $self->gff_version($gff_version) ) { | ||||
| 205 | $self->throw("Can't build a GFF object with the unknown version ". | ||||
| 206 | $gff_version); | ||||
| 207 | } | ||||
| 208 | $self->{'_first'} = 1; | ||||
| 209 | return $self; | ||||
| 210 | } | ||||
| 211 | |||||
| 212 | |||||
| 213 | =head2 _parse_header | ||||
| 214 | |||||
| 215 | Title : _parse_header | ||||
| 216 | Usage : $gffio->_parse_header() | ||||
| 217 | Function: used to turn parse GFF header lines. currently | ||||
| 218 | produces Bio::LocatableSeq objects from ##sequence-region | ||||
| 219 | lines | ||||
| 220 | Returns : 1 on success | ||||
| 221 | Args : none | ||||
| 222 | |||||
| 223 | |||||
| 224 | =cut | ||||
| 225 | |||||
| 226 | sub _parse_header{ | ||||
| 227 | my ($self) = @_; | ||||
| 228 | |||||
| 229 | my @unhandled; | ||||
| 230 | local $^W = 0; # hide warnings when we try and parse from a file opened | ||||
| 231 | # for writing - there isn't really a better way to do | ||||
| 232 | # AFAIK - cannot detech if a FH is read or write. | ||||
| 233 | while(my $line = $self->_readline()){ | ||||
| 234 | my $handled = 0; | ||||
| 235 | next if /^\s+$/; | ||||
| 236 | if($line =~ /^\#\#sequence-region\s+(\S+)\s+(\S+)\s+(\S+)\s*/){ | ||||
| 237 | my($seqid,$start,$end) = ($1,$2,$3); | ||||
| 238 | push @{ $self->{'segments'} }, Bio::LocatableSeq->new( | ||||
| 239 | -id => unescape($seqid), | ||||
| 240 | -start => $start, | ||||
| 241 | -end => $end, | ||||
| 242 | -length => ($end - $start + 1), ## make the length explicit | ||||
| 243 | ); | ||||
| 244 | $handled = 1; | ||||
| 245 | } elsif($line =~ /^(\#\#feature-ontology)/) { | ||||
| 246 | #to be implemented | ||||
| 247 | $self->warn("$1 header tag parsing unimplemented"); | ||||
| 248 | } elsif($line =~ /^(\#\#attribute-ontology)/) { | ||||
| 249 | #to be implemented | ||||
| 250 | $self->warn("$1 header tag parsing unimplemented"); | ||||
| 251 | } elsif($line =~ /^(\#\#source-ontology)/) { | ||||
| 252 | #to be implemented | ||||
| 253 | $self->warn("$1 header tag parsing unimplemented"); | ||||
| 254 | } elsif($line =~ /^(\#\#\#)/) { | ||||
| 255 | #to be implemented | ||||
| 256 | $self->warn("$1 header tag parsing unimplemented"); | ||||
| 257 | } elsif($line =~ /^(\#\#FASTA)/) { | ||||
| 258 | # initial ##FASTA is optional - artemis does not use it | ||||
| 259 | $line = $self->_readline(); | ||||
| 260 | if ($line !~ /^\>(\S+)/) { | ||||
| 261 | $self->throw("##FASTA directive must be followed by fasta header, not: $line"); | ||||
| 262 | } | ||||
| 263 | } | ||||
| 264 | |||||
| 265 | if ($line =~ /^\>(.*)/) { | ||||
| 266 | # seq data can be at header or footer | ||||
| 267 | my $seq = $self->_parse_sequence($line); | ||||
| 268 | if ($seq) { | ||||
| 269 | $self->_seq_by_id_h->{$seq->primary_id} = $seq; | ||||
| 270 | } | ||||
| 271 | } | ||||
| 272 | |||||
| 273 | |||||
| 274 | if(!$handled){ | ||||
| 275 | push @unhandled, $line; | ||||
| 276 | } | ||||
| 277 | |||||
| 278 | #looks like the header is over! | ||||
| 279 | last unless $line =~ /^\#/; | ||||
| 280 | } | ||||
| 281 | |||||
| 282 | foreach my $line (@unhandled){ | ||||
| 283 | $self->_pushback($line); | ||||
| 284 | } | ||||
| 285 | |||||
| 286 | return 1; | ||||
| 287 | } | ||||
| 288 | |||||
| 289 | sub _parse_sequence { | ||||
| 290 | my ($self, $line) = @_; | ||||
| 291 | |||||
| 292 | if ($line =~ /^\>(.*)/) { | ||||
| 293 | |||||
| 294 | my $seqid = $1; | ||||
| 295 | $seqid =~ s/\s+$//; | ||||
| 296 | my $desc = ''; | ||||
| 297 | if ($seqid =~ /(\S+)\s+(.*)/) { | ||||
| 298 | ($seqid, $desc) = ($1,$2); | ||||
| 299 | } | ||||
| 300 | my $res = ''; | ||||
| 301 | while (my $line = $self->_readline) { | ||||
| 302 | if ($line =~ /^\#/) { | ||||
| 303 | last; | ||||
| 304 | } | ||||
| 305 | if ($line =~ /^\>/) { | ||||
| 306 | $self->_pushback($line); | ||||
| 307 | last; | ||||
| 308 | } | ||||
| 309 | $line =~ s/\s//g; | ||||
| 310 | $res .= $line; | ||||
| 311 | } | ||||
| 312 | return if $self->ignore_sequence; | ||||
| 313 | |||||
| 314 | my $seqfactory = Bio::Seq::SeqFactory->new('Bio::Seq'); | ||||
| 315 | my $seq = $seqfactory->create(-seq=>$res, | ||||
| 316 | -id=>$seqid, | ||||
| 317 | -desc=>$desc); | ||||
| 318 | $seq->accession_number($seqid); | ||||
| 319 | if ($self->features_attached_to_seqs) { | ||||
| 320 | my @feats = | ||||
| 321 | @{$self->_feature_idx_by_seq_id->{$seqid}}; | ||||
| 322 | $seq->add_SeqFeature($_) foreach @feats; | ||||
| 323 | @{$self->_feature_idx_by_seq_id->{$seqid}} = (); | ||||
| 324 | } | ||||
| 325 | return $seq; | ||||
| 326 | } | ||||
| 327 | else { | ||||
| 328 | $self->throw("expected fasta header, not: $line"); | ||||
| 329 | } | ||||
| 330 | } | ||||
| 331 | |||||
| 332 | |||||
| 333 | =head2 next_segment | ||||
| 334 | |||||
| 335 | Title : next_segment | ||||
| 336 | Usage : my $seq = $gffio->next_segment; | ||||
| 337 | Function: Returns a Bio::LocatableSeq object corresponding to a | ||||
| 338 | GFF "##sequence-region" header line. | ||||
| 339 | Example : | ||||
| 340 | Returns : A Bio::LocatableSeq object, or undef if | ||||
| 341 | there are no more sequences. | ||||
| 342 | Args : none | ||||
| 343 | |||||
| 344 | |||||
| 345 | =cut | ||||
| 346 | |||||
| 347 | sub next_segment{ | ||||
| 348 | my ($self,@args) = @_; | ||||
| 349 | return shift @{ $self->{'segments'} } if defined $self->{'segments'}; | ||||
| 350 | return; | ||||
| 351 | } | ||||
| 352 | |||||
| 353 | |||||
| 354 | =head2 next_feature | ||||
| 355 | |||||
| 356 | Title : next_feature | ||||
| 357 | Usage : $seqfeature = $gffio->next_feature(); | ||||
| 358 | Function: Returns the next feature available in the input file or stream, or | ||||
| 359 | undef if there are no more features. | ||||
| 360 | Example : | ||||
| 361 | Returns : A Bio::SeqFeatureI implementing object, or undef if there are no | ||||
| 362 | more features. | ||||
| 363 | Args : none | ||||
| 364 | |||||
| 365 | =cut | ||||
| 366 | |||||
| 367 | sub next_feature { | ||||
| 368 | my ($self) = @_; | ||||
| 369 | |||||
| 370 | my $gff_string; | ||||
| 371 | |||||
| 372 | # be graceful about empty lines or comments, and make sure we return undef | ||||
| 373 | # if the input's consumed | ||||
| 374 | while(($gff_string = $self->_readline()) && defined($gff_string)) { | ||||
| 375 | if ($gff_string =~ /^\#\#\#/) { | ||||
| 376 | # all forward refs have been seen; TODO | ||||
| 377 | } | ||||
| 378 | next if($gff_string =~ /^\#/ || $gff_string =~ /^\s*$/ || | ||||
| 379 | $gff_string =~ m{^//}); | ||||
| 380 | |||||
| 381 | while ($gff_string =~ /^\>(.+)/) { | ||||
| 382 | # fasta can be in header or footer | ||||
| 383 | my $seq = $self->_parse_sequence($gff_string); | ||||
| 384 | if ($seq) { | ||||
| 385 | $self->_seq_by_id_h->{$seq->primary_id} = $seq; | ||||
| 386 | $gff_string = $self->_readline; | ||||
| 387 | last unless $gff_string; | ||||
| 388 | } | ||||
| 389 | } | ||||
| 390 | last; | ||||
| 391 | } | ||||
| 392 | return unless $gff_string; | ||||
| 393 | |||||
| 394 | my $feat = Bio::SeqFeature::Generic->new(); | ||||
| 395 | $self->from_gff_string($feat, $gff_string); | ||||
| 396 | |||||
| 397 | if ($self->features_attached_to_seqs) { | ||||
| 398 | push(@{$self->_feature_idx_by_seq_id->{$feat->seq_id}}, | ||||
| 399 | $feat); | ||||
| 400 | } | ||||
| 401 | |||||
| 402 | return $feat; | ||||
| 403 | } | ||||
| 404 | |||||
| 405 | sub _feature_idx_by_seq_id { | ||||
| 406 | my $self = shift; | ||||
| 407 | $self->{__feature_idx_by_seq_id} = shift if @_; | ||||
| 408 | $self->{__feature_idx_by_seq_id} = {} | ||||
| 409 | unless $self->{__feature_idx_by_seq_id}; | ||||
| 410 | return $self->{__feature_idx_by_seq_id}; | ||||
| 411 | } | ||||
| 412 | |||||
| 413 | |||||
| 414 | =head2 from_gff_string | ||||
| 415 | |||||
| 416 | Title : from_gff_string | ||||
| 417 | Usage : $gff->from_gff_string($feature, $gff_string); | ||||
| 418 | Function: Sets properties of a SeqFeatureI object from a GFF-formatted | ||||
| 419 | string. Interpretation of the string depends on the version | ||||
| 420 | that has been specified at initialization. | ||||
| 421 | |||||
| 422 | This method is used by next_feature(). It actually dispatches to | ||||
| 423 | one of the version-specific (private) methods. | ||||
| 424 | Example : | ||||
| 425 | Returns : void | ||||
| 426 | Args : A Bio::SeqFeatureI implementing object to be initialized | ||||
| 427 | The GFF-formatted string to initialize it from | ||||
| 428 | |||||
| 429 | =cut | ||||
| 430 | |||||
| 431 | sub from_gff_string { | ||||
| 432 | my ($self, $feat, $gff_string) = @_; | ||||
| 433 | |||||
| 434 | if($self->gff_version() == 1) { | ||||
| 435 | return $self->_from_gff1_string($feat, $gff_string); | ||||
| 436 | } elsif( $self->gff_version() == 3 ) { | ||||
| 437 | return $self->_from_gff3_string($feat, $gff_string); | ||||
| 438 | } else { | ||||
| 439 | return $self->_from_gff2_string($feat, $gff_string); | ||||
| 440 | } | ||||
| 441 | } | ||||
| 442 | |||||
| 443 | |||||
| 444 | =head2 _from_gff1_string | ||||
| 445 | |||||
| 446 | Title : _from_gff1_string | ||||
| 447 | Usage : | ||||
| 448 | Function: | ||||
| 449 | Example : | ||||
| 450 | Returns : void | ||||
| 451 | Args : A Bio::SeqFeatureI implementing object to be initialized | ||||
| 452 | The GFF-formatted string to initialize it from | ||||
| 453 | |||||
| 454 | =cut | ||||
| 455 | |||||
| 456 | sub _from_gff1_string { | ||||
| 457 | my ($gff, $feat, $string) = @_; | ||||
| 458 | chomp $string; | ||||
| 459 | my ($seqname, $source, $primary, $start, $end, $score, | ||||
| 460 | $strand, $frame, @group) = split(/\t/, $string); | ||||
| 461 | |||||
| 462 | if ( !defined $frame ) { | ||||
| 463 | $feat->throw("[$string] does not look like GFF to me"); | ||||
| 464 | } | ||||
| 465 | $frame = 0 unless( $frame =~ /^\d+$/); | ||||
| 466 | $feat->seq_id($seqname); | ||||
| 467 | $feat->source_tag($source); | ||||
| 468 | $feat->primary_tag($primary); | ||||
| 469 | $feat->start($start); | ||||
| 470 | $feat->end($end); | ||||
| 471 | $feat->frame($frame); | ||||
| 472 | if ( $score eq '.' ) { | ||||
| 473 | #$feat->score(undef); | ||||
| 474 | } else { | ||||
| 475 | $feat->score($score); | ||||
| 476 | } | ||||
| 477 | if ( $strand eq '-' ) { $feat->strand(-1); } | ||||
| 478 | if ( $strand eq '+' ) { $feat->strand(1); } | ||||
| 479 | if ( $strand eq '.' ) { $feat->strand(0); } | ||||
| 480 | foreach my $g ( @group ) { | ||||
| 481 | if ( $g =~ /(\S+)=(\S+)/ ) { | ||||
| 482 | my $tag = $1; | ||||
| 483 | my $value = $2; | ||||
| 484 | $feat->add_tag_value($1, $2); | ||||
| 485 | } else { | ||||
| 486 | $feat->add_tag_value('group', $g); | ||||
| 487 | } | ||||
| 488 | } | ||||
| 489 | } | ||||
| 490 | |||||
| 491 | |||||
| 492 | =head2 _from_gff2_string | ||||
| 493 | |||||
| 494 | Title : _from_gff2_string | ||||
| 495 | Usage : | ||||
| 496 | Function: | ||||
| 497 | Example : | ||||
| 498 | Returns : void | ||||
| 499 | Args : A Bio::SeqFeatureI implementing object to be initialized | ||||
| 500 | The GFF2-formatted string to initialize it from | ||||
| 501 | |||||
| 502 | |||||
| 503 | =cut | ||||
| 504 | |||||
| 505 | sub _from_gff2_string { | ||||
| 506 | my ($gff, $feat, $string) = @_; | ||||
| 507 | chomp($string); | ||||
| 508 | |||||
| 509 | # according to the Sanger website, GFF2 should be single-tab | ||||
| 510 | # separated elements, and the free-text at the end should contain | ||||
| 511 | # text-translated tab symbols but no "real" tabs, so splitting on | ||||
| 512 | # \t is safe, and $attribs gets the entire attributes field to be | ||||
| 513 | # parsed later | ||||
| 514 | |||||
| 515 | # sendu: but the tag value pair can (should?) be separated by a tab. The | ||||
| 516 | # 'no tabs' thing seems to apply only to the free text that is allowed for | ||||
| 517 | # the value | ||||
| 518 | |||||
| 519 | my ($seqname, $source, $primary, $start, | ||||
| 520 | $end, $score, $strand, $frame, @attribs) = split(/\t+/, $string); | ||||
| 521 | my $attribs = join ' ', @attribs; | ||||
| 522 | |||||
| 523 | if ( !defined $frame ) { | ||||
| 524 | $feat->throw("[$string] does not look like GFF2 to me"); | ||||
| 525 | } | ||||
| 526 | $feat->seq_id($seqname); | ||||
| 527 | $feat->source_tag($source); | ||||
| 528 | $feat->primary_tag($primary); | ||||
| 529 | $feat->start($start); | ||||
| 530 | $feat->end($end); | ||||
| 531 | $feat->frame($frame); | ||||
| 532 | if ( $score eq '.' ) { | ||||
| 533 | # $feat->score(undef); | ||||
| 534 | } else { | ||||
| 535 | $feat->score($score); | ||||
| 536 | } | ||||
| 537 | if ( $strand eq '-' ) { $feat->strand(-1); } | ||||
| 538 | if ( $strand eq '+' ) { $feat->strand(1); } | ||||
| 539 | if ( $strand eq '.' ) { $feat->strand(0); } | ||||
| 540 | |||||
| 541 | |||||
| 542 | # <Begin Inefficient Code from Mark Wilkinson> | ||||
| 543 | # this routine is necessay to allow the presence of semicolons in | ||||
| 544 | # quoted text Semicolons are the delimiting character for new | ||||
| 545 | # tag/value attributes. it is more or less a "state" machine, with | ||||
| 546 | # the "quoted" flag going up and down as we pass thorugh quotes to | ||||
| 547 | # distinguish free-text semicolon and hash symbols from GFF control | ||||
| 548 | # characters | ||||
| 549 | |||||
| 550 | my $flag = 0; # this could be changed to a bit and just be twiddled | ||||
| 551 | my @parsed; | ||||
| 552 | |||||
| 553 | # run through each character one at a time and check it | ||||
| 554 | # NOTE: changed to foreach loop which is more efficient in perl | ||||
| 555 | # --jasons | ||||
| 556 | for my $a ( split //, $attribs ) { | ||||
| 557 | # flag up on entering quoted text, down on leaving it | ||||
| 558 | if( $a eq '"') { $flag = ( $flag == 0 ) ? 1:0 } | ||||
| 559 | elsif( $a eq ';' && $flag ) { $a = "INSERT_SEMICOLON_HERE"} | ||||
| 560 | elsif( $a eq '#' && ! $flag ) { last } | ||||
| 561 | push @parsed, $a; | ||||
| 562 | } | ||||
| 563 | $attribs = join "", @parsed; # rejoin into a single string | ||||
| 564 | |||||
| 565 | # <End Inefficient Code> | ||||
| 566 | # Please feel free to fix this and make it more "perlish" | ||||
| 567 | |||||
| 568 | my @key_vals = split /;/, $attribs; # attributes are semicolon-delimited | ||||
| 569 | |||||
| 570 | foreach my $pair ( @key_vals ) { | ||||
| 571 | # replace semicolons that were removed from free-text above. | ||||
| 572 | $pair =~ s/INSERT_SEMICOLON_HERE/;/g; | ||||
| 573 | |||||
| 574 | # separate the key from the value | ||||
| 575 | my ($blank, $key, $values) = split /^\s*([\w\d]+)\s/, $pair; | ||||
| 576 | |||||
| 577 | if( defined $values ) { | ||||
| 578 | my @values; | ||||
| 579 | # free text is quoted, so match each free-text block | ||||
| 580 | # and remove it from the $values string | ||||
| 581 | while ($values =~ s/"(.*?)"//){ | ||||
| 582 | # and push it on to the list of values (tags may have | ||||
| 583 | # more than one value... and the value may be undef) | ||||
| 584 | push @values, $1; | ||||
| 585 | } | ||||
| 586 | |||||
| 587 | # and what is left over should be space-separated | ||||
| 588 | # non-free-text values | ||||
| 589 | |||||
| 590 | my @othervals = split /\s+/, $values; | ||||
| 591 | foreach my $othervalue(@othervals){ | ||||
| 592 | # get rid of any empty strings which might | ||||
| 593 | # result from the split | ||||
| 594 | if (CORE::length($othervalue) > 0) {push @values, $othervalue} | ||||
| 595 | } | ||||
| 596 | |||||
| 597 | foreach my $value(@values){ | ||||
| 598 | $feat->add_tag_value($key, $value); | ||||
| 599 | } | ||||
| 600 | } | ||||
| 601 | } | ||||
| 602 | } | ||||
| 603 | |||||
| 604 | |||||
| 605 | sub _from_gff3_string { | ||||
| 606 | my ($gff, $feat, $string) = @_; | ||||
| 607 | chomp($string); | ||||
| 608 | |||||
| 609 | # according to the now nearly final GFF3 spec, columns should | ||||
| 610 | # be tab separated, allowing unescaped spaces to occur in | ||||
| 611 | # column 9 | ||||
| 612 | |||||
| 613 | my ($seqname, $source, $primary, $start, $end, | ||||
| 614 | $score, $strand, $frame, $groups) = split(/\t/, $string); | ||||
| 615 | |||||
| 616 | if ( ! defined $frame ) { | ||||
| 617 | $feat->throw("[$string] does not look like GFF3 to me"); | ||||
| 618 | } | ||||
| 619 | $feat->seq_id($seqname); | ||||
| 620 | $feat->source_tag($source); | ||||
| 621 | $feat->primary_tag($primary); | ||||
| 622 | $feat->start($start); | ||||
| 623 | $feat->end($end); | ||||
| 624 | $feat->frame($frame); | ||||
| 625 | if ( $score eq '.' ) { | ||||
| 626 | #$feat->score(undef); | ||||
| 627 | } else { | ||||
| 628 | $feat->score($score); | ||||
| 629 | } | ||||
| 630 | if ( $strand eq '-' ) { $feat->strand(-1); } | ||||
| 631 | if ( $strand eq '+' ) { $feat->strand(1); } | ||||
| 632 | if ( $strand eq '.' ) { $feat->strand(0); } | ||||
| 633 | my @groups = split(/\s*;\s*/, $groups); | ||||
| 634 | |||||
| 635 | for my $group (@groups) { | ||||
| 636 | my ($tag,$value) = split /=/,$group; | ||||
| 637 | $tag = unescape($tag); | ||||
| 638 | my @values = map {unescape($_)} split /,/,$value; | ||||
| 639 | for my $v ( @values ) { $feat->add_tag_value($tag,$v); } | ||||
| 640 | } | ||||
| 641 | } | ||||
| 642 | |||||
| 643 | # taken from Bio::DB::GFF | ||||
| 644 | sub unescape { | ||||
| 645 | my $v = shift; | ||||
| 646 | $v =~ tr/+/ /; | ||||
| 647 | $v =~ s/%([0-9a-fA-F]{2})/chr hex($1)/ge; | ||||
| 648 | return $v; | ||||
| 649 | } | ||||
| 650 | |||||
| 651 | |||||
| 652 | =head2 write_feature | ||||
| 653 | |||||
| 654 | Title : write_feature | ||||
| 655 | Usage : $gffio->write_feature($feature); | ||||
| 656 | Function: Writes the specified SeqFeatureI object in GFF format to the stream | ||||
| 657 | associated with this instance. | ||||
| 658 | Returns : none | ||||
| 659 | Args : An array of Bio::SeqFeatureI implementing objects to be serialized | ||||
| 660 | |||||
| 661 | =cut | ||||
| 662 | |||||
| 663 | sub write_feature { | ||||
| 664 | my ($self, @features) = @_; | ||||
| 665 | return unless @features; | ||||
| 666 | if( $self->{'_first'} && $self->gff_version() == 3 ) { | ||||
| 667 | $self->_print("##gff-version 3\n"); | ||||
| 668 | } | ||||
| 669 | $self->{'_first'} = 0; | ||||
| 670 | foreach my $feature ( @features ) { | ||||
| 671 | $self->_print($self->gff_string($feature)."\n"); | ||||
| 672 | } | ||||
| 673 | } | ||||
| 674 | |||||
| 675 | |||||
| 676 | =head2 gff_string | ||||
| 677 | |||||
| 678 | Title : gff_string | ||||
| 679 | Usage : $gffstr = $gffio->gff_string($feature); | ||||
| 680 | Function: Obtain the GFF-formatted representation of a SeqFeatureI object. | ||||
| 681 | The formatting depends on the version specified at initialization. | ||||
| 682 | |||||
| 683 | This method is used by write_feature(). It actually dispatches to | ||||
| 684 | one of the version-specific (private) methods. | ||||
| 685 | Example : | ||||
| 686 | Returns : A GFF-formatted string representation of the SeqFeature | ||||
| 687 | Args : A Bio::SeqFeatureI implementing object to be GFF-stringified | ||||
| 688 | |||||
| 689 | =cut | ||||
| 690 | |||||
| 691 | sub gff_string{ | ||||
| 692 | my ($self, $feature) = @_; | ||||
| 693 | |||||
| 694 | if($self->gff_version() == 1) { | ||||
| 695 | return $self->_gff1_string($feature); | ||||
| 696 | } elsif( $self->gff_version() == 3 ) { | ||||
| 697 | return $self->_gff3_string($feature); | ||||
| 698 | } elsif( $self->gff_version() == 2.5 ) { | ||||
| 699 | return $self->_gff25_string($feature); | ||||
| 700 | } else { | ||||
| 701 | return $self->_gff2_string($feature); | ||||
| 702 | } | ||||
| 703 | } | ||||
| 704 | |||||
| 705 | |||||
| 706 | =head2 _gff1_string | ||||
| 707 | |||||
| 708 | Title : _gff1_string | ||||
| 709 | Usage : $gffstr = $gffio->_gff1_string | ||||
| 710 | Function: | ||||
| 711 | Example : | ||||
| 712 | Returns : A GFF1-formatted string representation of the SeqFeature | ||||
| 713 | Args : A Bio::SeqFeatureI implementing object to be GFF-stringified | ||||
| 714 | |||||
| 715 | =cut | ||||
| 716 | |||||
| 717 | sub _gff1_string{ | ||||
| 718 | my ($gff, $feat) = @_; | ||||
| 719 | my ($str,$score,$frame,$name,$strand); | ||||
| 720 | |||||
| 721 | if( $feat->can('score') ) { | ||||
| 722 | $score = $feat->score(); | ||||
| 723 | } | ||||
| 724 | $score = '.' unless defined $score; | ||||
| 725 | |||||
| 726 | if( $feat->can('frame') ) { | ||||
| 727 | $frame = $feat->frame(); | ||||
| 728 | } | ||||
| 729 | $frame = '.' unless defined $frame; | ||||
| 730 | |||||
| 731 | $strand = $feat->strand(); | ||||
| 732 | if(! $strand) { | ||||
| 733 | $strand = "."; | ||||
| 734 | } elsif( $strand == 1 ) { | ||||
| 735 | $strand = '+'; | ||||
| 736 | } elsif ( $feat->strand == -1 ) { | ||||
| 737 | $strand = '-'; | ||||
| 738 | } | ||||
| 739 | |||||
| 740 | if( $feat->can('seqname') ) { | ||||
| 741 | $name = $feat->seq_id(); | ||||
| 742 | $name ||= 'SEQ'; | ||||
| 743 | } else { | ||||
| 744 | $name = 'SEQ'; | ||||
| 745 | } | ||||
| 746 | |||||
| 747 | $str = join("\t", | ||||
| 748 | $name, | ||||
| 749 | $feat->source_tag, | ||||
| 750 | $feat->primary_tag, | ||||
| 751 | $feat->start, | ||||
| 752 | $feat->end, | ||||
| 753 | $score, | ||||
| 754 | $strand, | ||||
| 755 | $frame); | ||||
| 756 | |||||
| 757 | foreach my $tag ( $feat->get_all_tags ) { | ||||
| 758 | next if exists $SKIPPED_TAGS{$tag}; | ||||
| 759 | foreach my $value ( $feat->get_tag_values($tag) ) { | ||||
| 760 | $str .= " $tag=$value" if $value; | ||||
| 761 | } | ||||
| 762 | } | ||||
| 763 | |||||
| 764 | return $str; | ||||
| 765 | } | ||||
| 766 | |||||
| 767 | |||||
| 768 | =head2 _gff2_string | ||||
| 769 | |||||
| 770 | Title : _gff2_string | ||||
| 771 | Usage : $gffstr = $gffio->_gff2_string | ||||
| 772 | Function: | ||||
| 773 | Example : | ||||
| 774 | Returns : A GFF2-formatted string representation of the SeqFeature | ||||
| 775 | Args : A Bio::SeqFeatureI implementing object to be GFF2-stringified | ||||
| 776 | |||||
| 777 | =cut | ||||
| 778 | |||||
| 779 | sub _gff2_string{ | ||||
| 780 | my ($gff, $origfeat) = @_; | ||||
| 781 | my $feat; | ||||
| 782 | if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
| 783 | $feat = $origfeat->feature2; | ||||
| 784 | } else { | ||||
| 785 | $feat = $origfeat; | ||||
| 786 | } | ||||
| 787 | my ($str1, $str2,$score,$frame,$name,$strand); | ||||
| 788 | |||||
| 789 | if( $feat->can('score') ) { | ||||
| 790 | $score = $feat->score(); | ||||
| 791 | } | ||||
| 792 | $score = '.' unless defined $score; | ||||
| 793 | |||||
| 794 | if( $feat->can('frame') ) { | ||||
| 795 | $frame = $feat->frame(); | ||||
| 796 | } | ||||
| 797 | $frame = '.' unless defined $frame; | ||||
| 798 | |||||
| 799 | $strand = $feat->strand(); | ||||
| 800 | if(! $strand) { | ||||
| 801 | $strand = "."; | ||||
| 802 | } elsif( $strand == 1 ) { | ||||
| 803 | $strand = '+'; | ||||
| 804 | } elsif ( $feat->strand == -1 ) { | ||||
| 805 | $strand = '-'; | ||||
| 806 | } | ||||
| 807 | |||||
| 808 | if( $feat->can('seqname') ) { | ||||
| 809 | $name = $feat->seq_id(); | ||||
| 810 | } | ||||
| 811 | $name ||= 'SEQ'; | ||||
| 812 | |||||
| 813 | $str1 = join("\t", | ||||
| 814 | $name, | ||||
| 815 | $feat->source_tag(), | ||||
| 816 | $feat->primary_tag(), | ||||
| 817 | $feat->start(), | ||||
| 818 | $feat->end(), | ||||
| 819 | $score, | ||||
| 820 | $strand, | ||||
| 821 | $frame); | ||||
| 822 | # the routine below is the only modification I made to the original | ||||
| 823 | # ->gff_string routine (above) as on November 17th, 2000, the | ||||
| 824 | # Sanger webpage describing GFF2 format reads: "From version 2 | ||||
| 825 | # onwards, the attribute field must have a tag value structure | ||||
| 826 | # following the syntax used within objects in a .ace file, | ||||
| 827 | # flattened onto one line by semicolon separators. Tags must be | ||||
| 828 | # standard identifiers ([A-Za-z][A-Za-z0-9_]*). Free text values | ||||
| 829 | # must be quoted with double quotes". | ||||
| 830 | # MW | ||||
| 831 | |||||
| 832 | my @group; | ||||
| 833 | |||||
| 834 | foreach my $tag ( $feat->get_all_tags ) { | ||||
| 835 | next if exists $SKIPPED_TAGS{$tag}; | ||||
| 836 | my @v; | ||||
| 837 | foreach my $value ( $feat->get_tag_values($tag) ) { | ||||
| 838 | unless( defined $value && length($value) ) { | ||||
| 839 | # quote anything other than valid tag/value characters | ||||
| 840 | $value = '""'; | ||||
| 841 | } elsif ($value =~ /[^A-Za-z0-9_]/){ | ||||
| 842 | # substitute tab and newline chars by their UNIX equivalent | ||||
| 843 | $value =~ s/\t/\\t/g; | ||||
| 844 | $value =~ s/\n/\\n/g; | ||||
| 845 | $value = '"' . $value . '" '; | ||||
| 846 | } | ||||
| 847 | push @v, $value; | ||||
| 848 | # for this tag (allowed in GFF2 and .ace format) | ||||
| 849 | } | ||||
| 850 | push @group, "$tag ".join(" ", @v); | ||||
| 851 | } | ||||
| 852 | |||||
| 853 | $str2 .= join(' ; ', @group); | ||||
| 854 | # Add Target information for Feature Pairs | ||||
| 855 | if( ! $feat->has_tag('Target') && # This is a bad hack IMHO | ||||
| 856 | ! $feat->has_tag('Group') && | ||||
| 857 | $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { | ||||
| 858 | $str2 = sprintf("Target %s %d %d", $origfeat->feature1->seq_id, | ||||
| 859 | ( $origfeat->feature1->strand < 0 ? | ||||
| 860 | ( $origfeat->feature1->end, | ||||
| 861 | $origfeat->feature1->start) : | ||||
| 862 | ( $origfeat->feature1->start, | ||||
| 863 | $origfeat->feature1->end) | ||||
| 864 | )) . ($str2?" ; ".$str2:""); # need to put Target information before other tag/value pairs - mw | ||||
| 865 | } | ||||
| 866 | return $str1."\t".$str2; | ||||
| 867 | } | ||||
| 868 | |||||
| 869 | |||||
| 870 | =head2 _gff25_string | ||||
| 871 | |||||
| 872 | Title : _gff25_string | ||||
| 873 | Usage : $gffstr = $gffio->_gff2_string | ||||
| 874 | Function: To get a format of GFF that is peculiar to Gbrowse/Bio::DB::GFF | ||||
| 875 | Example : | ||||
| 876 | Returns : A GFF2.5-formatted string representation of the SeqFeature | ||||
| 877 | Args : A Bio::SeqFeatureI implementing object to be GFF2.5-stringified | ||||
| 878 | |||||
| 879 | =cut | ||||
| 880 | |||||
| 881 | sub _gff25_string { | ||||
| 882 | my ($gff, $origfeat) = @_; | ||||
| 883 | my $feat; | ||||
| 884 | if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
| 885 | $feat = $origfeat->feature2; | ||||
| 886 | } else { | ||||
| 887 | $feat = $origfeat; | ||||
| 888 | } | ||||
| 889 | my ($str1, $str2,$score,$frame,$name,$strand); | ||||
| 890 | |||||
| 891 | if( $feat->can('score') ) { | ||||
| 892 | $score = $feat->score(); | ||||
| 893 | } | ||||
| 894 | $score = '.' unless defined $score; | ||||
| 895 | |||||
| 896 | if( $feat->can('frame') ) { | ||||
| 897 | $frame = $feat->frame(); | ||||
| 898 | } | ||||
| 899 | $frame = '.' unless defined $frame; | ||||
| 900 | |||||
| 901 | $strand = $feat->strand(); | ||||
| 902 | if(! $strand) { | ||||
| 903 | $strand = "."; | ||||
| 904 | } elsif( $strand == 1 ) { | ||||
| 905 | $strand = '+'; | ||||
| 906 | } elsif ( $feat->strand == -1 ) { | ||||
| 907 | $strand = '-'; | ||||
| 908 | } | ||||
| 909 | |||||
| 910 | if( $feat->can('seqname') ) { | ||||
| 911 | $name = $feat->seq_id(); | ||||
| 912 | $name ||= 'SEQ'; | ||||
| 913 | } else { | ||||
| 914 | $name = 'SEQ'; | ||||
| 915 | } | ||||
| 916 | $str1 = join("\t", | ||||
| 917 | $name, | ||||
| 918 | $feat->source_tag(), | ||||
| 919 | $feat->primary_tag(), | ||||
| 920 | $feat->start(), | ||||
| 921 | $feat->end(), | ||||
| 922 | $score, | ||||
| 923 | $strand, | ||||
| 924 | $frame); | ||||
| 925 | |||||
| 926 | my @all_tags = $feat->all_tags; | ||||
| 927 | my @group; my @firstgroup; | ||||
| 928 | if (@all_tags) { # only play this game if it is worth playing... | ||||
| 929 | foreach my $tag ( @all_tags ) { | ||||
| 930 | my @v; | ||||
| 931 | foreach my $value ( $feat->get_tag_values($tag) ) { | ||||
| 932 | next if exists $SKIPPED_TAGS{$tag}; | ||||
| 933 | unless( defined $value && length($value) ) { | ||||
| 934 | $value = '""'; | ||||
| 935 | } elsif ($value =~ /[^A-Za-z0-9_]/){ | ||||
| 936 | $value =~ s/\t/\\t/g; # substitute tab and newline | ||||
| 937 | # characters | ||||
| 938 | $value =~ s/\n/\\n/g; # to their UNIX equivalents | ||||
| 939 | $value = '"' . $value . '" '; | ||||
| 940 | } # if the value contains | ||||
| 941 | # anything other than valid | ||||
| 942 | # tag/value characters, then | ||||
| 943 | # quote it | ||||
| 944 | push @v, $value; | ||||
| 945 | # for this tag (allowed in GFF2 and .ace format) | ||||
| 946 | } | ||||
| 947 | if (($tag eq 'Group') || ($tag eq 'Target')){ # hopefully we wont get both... | ||||
| 948 | push @firstgroup, "$tag ".join(" ", @v); | ||||
| 949 | } else { | ||||
| 950 | push @group, "$tag ".join(" ", @v); | ||||
| 951 | } | ||||
| 952 | } | ||||
| 953 | } | ||||
| 954 | $str2 = join(' ; ', (@firstgroup, @group)); | ||||
| 955 | # Add Target information for Feature Pairs | ||||
| 956 | if( ! $feat->has_tag('Target') && # This is a bad hack IMHO | ||||
| 957 | ! $feat->has_tag('Group') && | ||||
| 958 | $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { | ||||
| 959 | $str2 = sprintf("Target %s ; tstart %d ; tend %d", $origfeat->feature1->seq_id, | ||||
| 960 | ( $origfeat->feature1->strand < 0 ? | ||||
| 961 | ( $origfeat->feature1->end, | ||||
| 962 | $origfeat->feature1->start) : | ||||
| 963 | ( $origfeat->feature1->start, | ||||
| 964 | $origfeat->feature1->end) | ||||
| 965 | )) . ($str2?" ; ".$str2:""); # need to put the target info before other tag/value pairs - mw | ||||
| 966 | } | ||||
| 967 | return $str1 . "\t". $str2; | ||||
| 968 | } | ||||
| 969 | |||||
| 970 | |||||
| 971 | =head2 _gff3_string | ||||
| 972 | |||||
| 973 | Title : _gff3_string | ||||
| 974 | Usage : $gffstr = $gffio->_gff3_string | ||||
| 975 | Function: | ||||
| 976 | Example : | ||||
| 977 | Returns : A GFF3-formatted string representation of the SeqFeature | ||||
| 978 | Args : A Bio::SeqFeatureI implementing object to be GFF3-stringified | ||||
| 979 | |||||
| 980 | =cut | ||||
| 981 | |||||
| 982 | sub _gff3_string { | ||||
| 983 | my ($gff, $origfeat) = @_; | ||||
| 984 | my $feat; | ||||
| 985 | if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
| 986 | $feat = $origfeat->feature2; | ||||
| 987 | } else { | ||||
| 988 | $feat = $origfeat; | ||||
| 989 | } | ||||
| 990 | |||||
| 991 | my $ID = $gff->_incrementGFF3ID(); | ||||
| 992 | |||||
| 993 | my ($score,$frame,$name,$strand); | ||||
| 994 | |||||
| 995 | if( $feat->can('score') ) { | ||||
| 996 | $score = $feat->score(); | ||||
| 997 | } | ||||
| 998 | $score = '.' unless defined $score; | ||||
| 999 | |||||
| 1000 | if( $feat->can('frame') ) { | ||||
| 1001 | $frame = $feat->frame(); | ||||
| 1002 | } | ||||
| 1003 | $frame = '1' unless defined $frame; | ||||
| 1004 | |||||
| 1005 | $strand = $feat->strand(); | ||||
| 1006 | |||||
| 1007 | if(! $strand) { | ||||
| 1008 | $strand = "."; | ||||
| 1009 | } elsif( $strand == 1 ) { | ||||
| 1010 | $strand = '+'; | ||||
| 1011 | } elsif ( $feat->strand == -1 ) { | ||||
| 1012 | $strand = '-'; | ||||
| 1013 | } | ||||
| 1014 | |||||
| 1015 | if( $feat->can('seqname') ) { | ||||
| 1016 | $name = $feat->seq_id(); | ||||
| 1017 | $name ||= 'SEQ'; | ||||
| 1018 | } else { | ||||
| 1019 | $name = 'SEQ'; | ||||
| 1020 | } | ||||
| 1021 | |||||
| 1022 | my @groups; | ||||
| 1023 | |||||
| 1024 | # force leading ID and Parent tags | ||||
| 1025 | my @all_tags = grep { ! exists $GFF3_ID_Tags{$_} } $feat->all_tags; | ||||
| 1026 | for my $t ( sort { $GFF3_ID_Tags{$b} <=> $GFF3_ID_Tags{$a} } | ||||
| 1027 | keys %GFF3_ID_Tags ) { | ||||
| 1028 | unshift @all_tags, $t if $feat->has_tag($t); | ||||
| 1029 | } | ||||
| 1030 | |||||
| 1031 | for my $tag ( @all_tags ) { | ||||
| 1032 | next if exists $SKIPPED_TAGS{$tag}; | ||||
| 1033 | # next if $tag eq 'Target'; | ||||
| 1034 | if ($tag eq 'Target' && ! $origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
| 1035 | # simple Target,start,stop | ||||
| 1036 | my($target_id, $b,$e,$strand) = $feat->get_tag_values($tag); | ||||
| 1037 | next unless(defined($e) && defined($b) && $target_id); | ||||
| 1038 | ($b,$e)= ($e,$b) if(defined $strand && $strand<0); | ||||
| 1039 | $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; | ||||
| 1040 | push @groups, sprintf("Target=%s %d %d", $target_id,$b,$e); | ||||
| 1041 | next; | ||||
| 1042 | } | ||||
| 1043 | |||||
| 1044 | my $valuestr; | ||||
| 1045 | # a string which will hold one or more values | ||||
| 1046 | # for this tag, with quoted free text and | ||||
| 1047 | # space-separated individual values. | ||||
| 1048 | my @v; | ||||
| 1049 | for my $value ( $feat->get_tag_values($tag) ) { | ||||
| 1050 | if( defined $value && length($value) ) { | ||||
| 1051 | #$value =~ tr/ /+/; #spaces are allowed now | ||||
| 1052 | if ( ref $value eq 'Bio::Annotation::Comment') { | ||||
| 1053 | $value = $value->text; | ||||
| 1054 | } | ||||
| 1055 | |||||
| 1056 | if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) { | ||||
| 1057 | $value =~ s/\t/\\t/g; # substitute tab and newline | ||||
| 1058 | # characters | ||||
| 1059 | $value =~ s/\n/\\n/g; # to their UNIX equivalents | ||||
| 1060 | |||||
| 1061 | # Unescaped quotes are not allowed in GFF3 | ||||
| 1062 | # $value = '"' . $value . '"'; | ||||
| 1063 | } | ||||
| 1064 | $value =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; | ||||
| 1065 | } else { | ||||
| 1066 | # if it is completely empty, then just make empty double quotes | ||||
| 1067 | $value = '""'; | ||||
| 1068 | } | ||||
| 1069 | push @v, $value; | ||||
| 1070 | } | ||||
| 1071 | # can we figure out how to improve this? | ||||
| 1072 | $tag = lcfirst($tag) unless ( $tag =~ | ||||
| 1073 | /^(ID|Name|Alias|Parent|Gap|Target|Derives_from|Note|Dbxref|Ontology_term)$/); | ||||
| 1074 | |||||
| 1075 | push @groups, "$tag=".join(",",@v); | ||||
| 1076 | } | ||||
| 1077 | # Add Target information for Feature Pairs | ||||
| 1078 | if( $feat->has_tag('Target') && | ||||
| 1079 | ! $feat->has_tag('Group') && | ||||
| 1080 | $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { | ||||
| 1081 | |||||
| 1082 | my $target_id = $origfeat->feature1->seq_id; | ||||
| 1083 | $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; | ||||
| 1084 | |||||
| 1085 | push @groups, sprintf("Target=%s %d %d", | ||||
| 1086 | $target_id, | ||||
| 1087 | ( $origfeat->feature1->strand < 0 ? | ||||
| 1088 | ( $origfeat->feature1->end, | ||||
| 1089 | $origfeat->feature1->start) : | ||||
| 1090 | ( $origfeat->feature1->start, | ||||
| 1091 | $origfeat->feature1->end) | ||||
| 1092 | )); | ||||
| 1093 | } | ||||
| 1094 | |||||
| 1095 | # unshift @groups, "ID=autogenerated$ID" unless ($feat->has_tag('ID')); | ||||
| 1096 | if ( $feat->can('name') && defined($feat->name) ) { | ||||
| 1097 | # such as might be for Bio::DB::SeqFeature | ||||
| 1098 | unshift @groups, 'Name=' . $feat->name; | ||||
| 1099 | } | ||||
| 1100 | |||||
| 1101 | my $gff_string = ""; | ||||
| 1102 | if ($feat->location->isa("Bio::Location::SplitLocationI")) { | ||||
| 1103 | my @locs = $feat->location->each_Location; | ||||
| 1104 | foreach my $loc (@locs) { | ||||
| 1105 | $gff_string .= join("\t", | ||||
| 1106 | $name, | ||||
| 1107 | $feat->source_tag() || '.', | ||||
| 1108 | $feat->primary_tag(), | ||||
| 1109 | $loc->start(), | ||||
| 1110 | $loc->end(), | ||||
| 1111 | $score, | ||||
| 1112 | $strand, | ||||
| 1113 | $frame, | ||||
| 1114 | join(';', @groups)) . "\n"; | ||||
| 1115 | } | ||||
| 1116 | chop $gff_string; | ||||
| 1117 | return $gff_string; | ||||
| 1118 | } else { | ||||
| 1119 | $gff_string = join("\t", | ||||
| 1120 | $name, | ||||
| 1121 | $feat->source_tag() || '.', | ||||
| 1122 | $feat->primary_tag(), | ||||
| 1123 | $feat->start(), | ||||
| 1124 | $feat->end(), | ||||
| 1125 | $score, | ||||
| 1126 | $strand, | ||||
| 1127 | $frame, | ||||
| 1128 | join(';', @groups)); | ||||
| 1129 | } | ||||
| 1130 | return $gff_string; | ||||
| 1131 | } | ||||
| 1132 | |||||
| 1133 | |||||
| 1134 | =head2 gff_version | ||||
| 1135 | |||||
| 1136 | Title : _gff_version | ||||
| 1137 | Usage : $gffversion = $gffio->gff_version | ||||
| 1138 | Function: | ||||
| 1139 | Example : | ||||
| 1140 | Returns : The GFF version this parser will accept and emit. | ||||
| 1141 | Args : none | ||||
| 1142 | |||||
| 1143 | =cut | ||||
| 1144 | |||||
| 1145 | sub gff_version { | ||||
| 1146 | my ($self, $value) = @_; | ||||
| 1147 | if(defined $value && grep {$value == $_ } ( 1, 2, 2.5, 3)) { | ||||
| 1148 | $self->{'GFF_VERSION'} = $value; | ||||
| 1149 | } | ||||
| 1150 | return $self->{'GFF_VERSION'}; | ||||
| 1151 | } | ||||
| 1152 | |||||
| 1153 | |||||
| 1154 | # Make filehandles | ||||
| 1155 | |||||
| 1156 | =head2 newFh | ||||
| 1157 | |||||
| 1158 | Title : newFh | ||||
| 1159 | Usage : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') | ||||
| 1160 | Function: does a new() followed by an fh() | ||||
| 1161 | Example : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') | ||||
| 1162 | $feature = <$fh>; # read a feature object | ||||
| 1163 | print $fh $feature; # write a feature object | ||||
| 1164 | Returns : filehandle tied to the Bio::Tools::GFF class | ||||
| 1165 | Args : | ||||
| 1166 | |||||
| 1167 | =cut | ||||
| 1168 | |||||
| 1169 | sub newFh { | ||||
| 1170 | my $class = shift; | ||||
| 1171 | return unless my $self = $class->new(@_); | ||||
| 1172 | return $self->fh; | ||||
| 1173 | } | ||||
| 1174 | |||||
| 1175 | |||||
| 1176 | =head2 fh | ||||
| 1177 | |||||
| 1178 | Title : fh | ||||
| 1179 | Usage : $obj->fh | ||||
| 1180 | Function: | ||||
| 1181 | Example : $fh = $obj->fh; # make a tied filehandle | ||||
| 1182 | $feature = <$fh>; # read a feature object | ||||
| 1183 | print $fh $feature; # write a feature object | ||||
| 1184 | Returns : filehandle tied to Bio::Tools::GFF class | ||||
| 1185 | Args : none | ||||
| 1186 | |||||
| 1187 | =cut | ||||
| 1188 | |||||
| 1189 | |||||
| 1190 | sub fh { | ||||
| 1191 | my $self = shift; | ||||
| 1192 | my $class = ref($self) || $self; | ||||
| 1193 | my $s = Symbol::gensym; | ||||
| 1194 | tie $$s,$class,$self; | ||||
| 1195 | return $s; | ||||
| 1196 | } | ||||
| 1197 | |||||
| 1198 | # This accessor is used for accessing the Bio::Seq objects from a GFF3 | ||||
| 1199 | # file; if the file you are using has no sequence data you can ignore | ||||
| 1200 | # this accessor | ||||
| 1201 | |||||
| 1202 | # This accessor returns a hash reference containing Bio::Seq objects, | ||||
| 1203 | # indexed by Bio::Seq->primary_id | ||||
| 1204 | |||||
| 1205 | sub _seq_by_id_h { | ||||
| 1206 | my $self = shift; | ||||
| 1207 | |||||
| 1208 | return $self->{'_seq_by_id_h'} = shift if @_; | ||||
| 1209 | $self->{'_seq_by_id_h'} = {} | ||||
| 1210 | unless $self->{'_seq_by_id_h'}; | ||||
| 1211 | return $self->{'_seq_by_id_h'}; | ||||
| 1212 | } | ||||
| 1213 | |||||
| 1214 | |||||
| 1215 | =head2 get_seqs | ||||
| 1216 | |||||
| 1217 | Title : get_seqs | ||||
| 1218 | Usage : | ||||
| 1219 | Function: Returns all Bio::Seq objects populated by GFF3 file | ||||
| 1220 | Example : | ||||
| 1221 | Returns : | ||||
| 1222 | Args : | ||||
| 1223 | |||||
| 1224 | =cut | ||||
| 1225 | |||||
| 1226 | sub get_seqs { | ||||
| 1227 | my ($self,@args) = @_; | ||||
| 1228 | return values %{$self->_seq_by_id_h}; | ||||
| 1229 | } | ||||
| 1230 | |||||
| 1231 | |||||
| 1232 | =head2 features_attached_to_seqs | ||||
| 1233 | |||||
| 1234 | Title : features_attached_to_seqs | ||||
| 1235 | Usage : $obj->features_attached_to_seqs(1); | ||||
| 1236 | Function: For use with GFF3 containg sequence only | ||||
| 1237 | |||||
| 1238 | Setting this B<before> parsing ensures that all Bio::Seq object | ||||
| 1239 | created will have the appropriate features added to them | ||||
| 1240 | |||||
| 1241 | defaults to false (off) | ||||
| 1242 | |||||
| 1243 | Note that this mode will incur higher memory usage because features | ||||
| 1244 | will have to be cached until the relevant feature comes along | ||||
| 1245 | |||||
| 1246 | Example : | ||||
| 1247 | Returns : value of features_attached_to_seqs (a boolean) | ||||
| 1248 | Args : on set, new value (a boolean, optional) | ||||
| 1249 | |||||
| 1250 | |||||
| 1251 | =cut | ||||
| 1252 | |||||
| 1253 | sub features_attached_to_seqs{ | ||||
| 1254 | my $self = shift; | ||||
| 1255 | |||||
| 1256 | return $self->{'_features_attached_to_seqs'} = shift if @_; | ||||
| 1257 | return $self->{'_features_attached_to_seqs'}; | ||||
| 1258 | } | ||||
| 1259 | |||||
| 1260 | |||||
| 1261 | =head2 ignore_sequence | ||||
| 1262 | |||||
| 1263 | Title : ignore_sequence | ||||
| 1264 | Usage : $obj->ignore_sequence(1); | ||||
| 1265 | Function: For use with GFF3 containg sequence only | ||||
| 1266 | |||||
| 1267 | Setting this B<before> parsing means that all sequence data will be | ||||
| 1268 | ignored | ||||
| 1269 | |||||
| 1270 | Example : | ||||
| 1271 | Returns : value of ignore_sequence (a boolean) | ||||
| 1272 | Args : on set, new value (a boolean, optional) | ||||
| 1273 | |||||
| 1274 | =cut | ||||
| 1275 | |||||
| 1276 | sub ignore_sequence{ | ||||
| 1277 | my $self = shift; | ||||
| 1278 | |||||
| 1279 | return $self->{'_ignore_sequence'} = shift if @_; | ||||
| 1280 | return $self->{'_ignore_sequence'}; | ||||
| 1281 | } | ||||
| 1282 | |||||
| 1283 | |||||
| 1284 | sub DESTROY { | ||||
| 1285 | my $self = shift; | ||||
| 1286 | $self->close(); | ||||
| 1287 | } | ||||
| 1288 | |||||
| 1289 | sub TIEHANDLE { | ||||
| 1290 | my ($class,$val) = @_; | ||||
| 1291 | return bless {'gffio' => $val}, $class; | ||||
| 1292 | } | ||||
| 1293 | |||||
| 1294 | sub READLINE { | ||||
| 1295 | my $self = shift; | ||||
| 1296 | return $self->{'gffio'}->next_feature() || undef unless wantarray; | ||||
| 1297 | my (@list, $obj); | ||||
| 1298 | push @list, $obj while $obj = $self->{'gffio'}->next_feature(); | ||||
| 1299 | return @list; | ||||
| 1300 | } | ||||
| 1301 | |||||
| 1302 | sub PRINT { | ||||
| 1303 | my $self = shift; | ||||
| 1304 | $self->{'gffio'}->write_feature(@_); | ||||
| 1305 | } | ||||
| 1306 | |||||
| 1307 | 1 | 10µs | 1; | ||
| 1308 |