This file is indexed.

/usr/share/perl5/Boulder/Unigene.pm is in libboulder-perl 1.30-4.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  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
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
package Boulder::Unigene;
#
use Boulder::Stream;
require Exporter;
@ISA = qw(Exporter Boulder::Stream);
@EXPORT = ();
@EXPORT_OK = ();
use Carp;
$VERSION=1.0;
use constant DEFAULT_UNIGENE_PATH => '/data/unigene/Hs.dat';

=head1 NAME

Boulder::Unigene - Fetch Unigene data records as parsed Boulder Stones

=head1 SYNOPSIS

  # parse a file of Unigene records
  $ug = new Boulder::Unigene(-accessor=>'File',
                             -param => '/data/unigene/Hs.dat');
  while (my $s = $ug->get) {
    print $s->Identifier;
    print $s->Gene;
  }

  # parse flatfile records yourself
  open (UG,"/data/unigene/Hs.dat");
  local $/ = "*RECORD*";
  while (<UG>) {
     my $s = Boulder::Unigene->parse($_);
     # etc.
  }

=head1 DESCRIPTION

Boulder::Unigene provides retrieval and parsing services for UNIGENE records

Boulder::Unigene provides retrieval and parsing services for NCBI
Unigene records.  It returns Unigene entries in L<Stone>
format, allowing easy access to the various fields and values.
Boulder::Unigene is a descendent of Boulder::Stream, and provides a
stream-like interface to a series of Stone objects.

Access to Unigene is provided by one I<accessors>, which
give access to  local Unigene database.  When you
create a new Boulder::Unigene stream, you provide the
accessors, along with accessor-specific parameters that control what
entries to fetch.  The accessors is:

=over 2

=item File

This provides access to local Unigene entries by reading from a flat file
(typically Hs.dat file downloadable from NCBI's Ftp site).
The stream will return a Stone corresponding to each of the entries in 
the file, starting from the top of the file and working downward.  The 
parameter is the path to the local file.

=back

It is also possible to parse a single Unigene entry from a text string 
stored in a scalar variable, returning a Stone object.

=head2 Boulder::Unigene methods

This section lists the public methods that the I<Boulder::Unigene>
class makes available.

=over 4

=item new()

   # Local fetch via File
   $ug=new Boulder::Unigene(-accessor  =>  'File',
                            -param     =>  '/data/unigene/Hs.dat');

The new() method creates a new I<Boulder::Unigene> stream on the
accessor provided.  The only possible accessors is B<File>.  
If successful, the method returns the stream
object.  Otherwise it returns undef.

new() takes the following arguments:

	-accessor	Name of the accessor to use
	-param		Parameters to pass to the accessor

Specify the accessor to use with the B<-accessor> argument.  If not
specified, it defaults to B<File>.  

B<-param> is an accessor-specific argument.  The possibilities is:

For B<File>, the B<-param> argument must point to a string-valued
scalar, which will be interpreted as the path to the file to read
Unigene entries from.

=item get()

The get() method is inherited from I<Boulder::Stream>, and simply
returns the next parsed Unigene Stone, or undef if there is nothing
more to fetch.  It has the same semantics as the parent class,
including the ability to restrict access to certain top-level tags.

=item put()

The put() method is inherited from the parent Boulder::Stream class,
and will write the passed Stone to standard output in Boulder format.
This means that it is currently not possible to write a
Boulder::Unigene object back into Unigene flatfile form.

=back

=head1 OUTPUT TAGS

The tags returned by the parsing operation are taken from the names shown in the Flat file
Hs.dat since no better description of them is provided yet by the database source producer.

=head2 Top-Level Tags

These are tags that appear at the top level of the parsed Unigene
entry.

=over 4

=item Identifier

The Unigene identifier of this entry.  Identifier is a single-value tag.

Example:
       
      my $identifierNo = $s->Identifier;

=item Title

The Unigene title for this entry.

Example:
      my $titledef=$s->Title;

=item Gene
The Gene associated with   this Unigene entry

Example:
      my $thegene=$s->Gene;

=item Cytoband
The cytological band position of this entry

Example:
      my $thecytoband=$s->Cytoband;

=item Counts
The number of EST in this record

Example:
      my $thecounts=$s->Counts;

=item LocusLink
The id of the LocusLink entry associated with this record

Example:
      my $thelocuslink=$s->LocusLink;

=item Chromosome
This field contains a list, of the chromosomes numbers in which this entry has been linked

Example:
      my @theChromosome=$s->Chromosome;

=back

=head2 STS     
Multiple records in the form ^STS     ACC=XXXXXX NAME=YYYYYY

=over 4

=item ACC

=item NAME

=back

=head2 TXMAP
Multiple records in the form  ^TXMAP  XXXXXXX; MARKER=YYYYY; RHPANEL=ZZZZ

The TXMAP tag points to a Stone record that contains multiple
subtags.  Each subtag is the name of a feature which points, in turn,
to a Stone that describes the feature's location and other attributes.

Each feature will contain one or more of the following subtags:

=over 4

=item MARKER

=item RHPANEL

=back


=head2 PROTSIM
Multiple records in the form ^PROTSIM ORG=XXX; PROTID=DBID:YYY; PCT=ZZZ; ALN=QQQQ
Where DBID is 
	PID for indicate presence of GenPept identifier, 
	SP to indicate SWISSPROT identifier,
	PIR to indicate PIR identifier,
	PRF to indicate ???

=over 4

=item ORG

=item PROTID

=item PCT

=item ALN

=back

=head2 SEQUENCE
Multiple records in the form ^SEQUENCE ACC=XXX; NID=YYYY; PID = CLONE= END= LID=

=over

=item ACC

=item NID

=item PID

=item CLONE

=item END

=item LID

=back

=head1 SEE ALSO

L<Boulder>, L<Boulder::Blast>, L<Boulder::Genbank>

=head1 AUTHOR

Lincoln Stein <lstein@cshl.org>.
Luca I.G. Toldo <luca.toldo@merck.de>

Copyright (c) 1997 Lincoln D. Stein
Copyright (c) 1999 Luca I.G. Toldo

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

#
# Following did not require any changes compared to Genbank.pm
#
sub new  {
    my($package,@parameters) = @_;
    # superclass constructor
    my($self) = new Boulder::Stream;
    
    # figure out whether parameters are named.  Look for
    # an initial '-'
    if ($parameters[0]=~/^-/) {
	my(%parameters) = @parameters;
	$self->{'accessor'}=$parameters{'-accessor'} || 'File';
	$self->{'param'}=$parameters{'-param'};
	$self->{'OUT'}=$parameters{'-out'} || 'main::STDOUT';
    } else {
	$self->{'accessor'}='File';
	$self->{'param'}=[@parameters];
    }
    
    croak "Require parameters" unless defined($self->{'param'});
    $self->{'accessor'} = new {$self->{'accessor'}}($self->{'param'});
    
    return bless $self,$package;
}

#
# Following required no changes compared to Genbank.pm
#
sub read_record {
    my($self,@tags) = @_;
    my($s);

    if (wantarray) {
	my(@result);
	while (!$self->{'done'}) {
	    $s = $self->read_one_record(@tags);
	    next unless $s;
	    next if $query && !(&$query);
	    push(@result,$s);
	}
	return @result;
    } 

    # we get here if in a scalar context
    while (!$self->{'done'}) {
	$s = $self->read_one_record(@tags);
	next unless $s;
	return $s unless $query;
	return $s if &$query;
    }
    return undef;
}

#<LIGT>
# Here is everything new
#</LIGT>
sub parse {
  my $self = shift;
  my $record = shift;
  return unless $record;
  my $tags = shift;
  my %ok;
  %ok = map {$_ => 1} @$tags if ref($tags) eq 'ARRAY';
    my($s,@lines,$line,$accumulated,$key,$keyword,$value,$feature,@features, $label);
  
  $s = new Stone;
#<LIGT> following this line the parsing of the record must be done
#              each key-value pair is stored by the following command:
#	$self->_addToStone($key,$value,$stone,\%ok);
#
# Process new record lines
#
#
  (@recordlines)=split(/\n/,$record);
 undef $unigeneid, $title, $gene,$cytoband, $locuslink, $chromosome, $scount;
 undef $sts, $txmap,$protsim,$sequence;
 undef @sts,@txmaps,@protsims,@sequences;
  foreach $line  (@recordlines) {
    if      ($line=~/^ID/) {
     ($key,$unigeneid)=split(/\s+/,$line);
     $self->_addToStone('Identifier',$unigeneid,$s,\%ok);
    } elsif ($line=~/^TITLE/) {
     (@titles)=split(/\s+/,$line);
     shift @titles;
     $title=join(' ',@titles);
     $self->_addToStone('Title',$title,$s,\%ok);
    } elsif ($line=~/^GENE/) {
     ($key,$gene)=split(/\s+/,$line);
     $self->_addToStone('Gene',$gene,$s,\%ok);
    } elsif ($line=~/^CYTOBAND/) {
     ($key,$cytoband)=split(/\s+/,$line);
     $self->_addToStone('Cytoband',$cytoband,$s,\%ok);
    } elsif ($line=~/^LOCUSLINK/) {
     ($key,$locuslink)=split(/\s+/,$line);
     $self->_addToStone('Locuslink',$locuslink,$s,\%ok);
    } elsif ($line=~/^CHROMOSOME/) {
     ($key,$chromosome)=split(/\s+/,$line);
     $self->_addToStone('Chromosome',$chromosome,$s,\%ok);
    } elsif ($line=~/^SCOUNT/) {
     ($key,$scount)=split(/\s+/,$line);
     $self->_addToStone('Scount',$scount,$s,\%ok);
    } elsif ($line=~/^STS/) {
#STS ACC=XXX; NAME=YYY;
     (@sts)=split(/\s+/,$line); shift @sts;  $sts=join(' ',@sts);
     ($tmpacc,$tmpname)=split(/\s+/,$sts);
     ($jnk,$acc)=split(/\=/,$tmpacc);
     ($jnk,$name)=split(/\=/,$tmpname);

     undef @features;    
     $featurelabel="Accession"; $featurevalue=$name;
     $feature = {'label'=>$featurelabel,'value'=>$featurevalue};
     push(@features,$feature);
     $featurelabel="Name";
     $feature = {'label'=>$featurelabel,'value'=>$featurevalue};
     push(@features,$feature);

      $self->_addFeaturesToStone(\@features,_trim($'),$s,\%ok);
    } elsif ($line=~/^TXMAP/) {
#TXMAP  XXX; MARKER=YYY; RHPANEL=ZZZ;
     (@txmaps)=split(/\s+/,$line); shift @txmaps;  $txmap=join(' ',@txmaps);
#     $self->_addToStone('TXMAP',$txmap,$s,\%ok);
    undef @features;
     $self->_addFeaturesToStone(\@features,_trim($'),$s,\%ok);
    } elsif ($line=~/^PROTSIM/) {
#PROTSIM ORG=QQQ; PROTID=RRR; PCT=SSSS; ALN=TTTT;
     (@protsims)=split(/\s+/,$line); shift @protsims;  $protsim=join(' ',@protsims);
#     $self->_addToStone('PROTSIM',$protsim,$s,\%ok);
    undef @features;
     $self->_addFeaturesToStone(\@features,_trim($'),$s,\%ok);
    } elsif ($line=~/^SEQUENCE/) {
#SEQUENCE ACC=XXXX; NID=YYYY; PID=RRRRR; CLONE=QQQ; END=PPPP; LID=ZZZZ;
     (@sequences)=split(/\s+/,$line); shift @sequences;  $sequence=join(' ',@sequences);
#     $self->_addToStone('SEQUENCE',$sequence,$s,\%ok);
    undef @features;
     $self->_addFeaturesToStone(\@features,_trim($'),$s,\%ok);
   }
 }
#</LIGT>
  return $s;
}

#
# Following is unchanged from Genbank.pm
#
sub read_one_record {
  my($self,@tags) = @_;
  my(%ok);  
  my $accessor = $self->{'accessor'};
  my $record   = $accessor->fetch_next();
  unless ($record) {
    $self->{'done'}++;
    return undef;
  }

  return $self->parse($record,\@tags);
}

#
# Following is unchanged from Genbank.pm
#
sub _trim {
    my($v) = @_;
    $v=~s/^\s+//;
    $v=~s/\s+$//;
    return $v;
}

#
# Following is unchanged from Genbank.pm
#
sub _canonicalize {
  my $h = shift;
  substr($h,0)=~tr/a-z/A-Z/;
  substr($h,1,length($h)-1)=~tr/A-Z/a-z/;
  $h;
}

#
# Following is unchanged from Genbank.pm
#
sub _addToStone {
    my($self,$xlabel,$value,$stone,$ok) = @_;
    return unless !%{$ok} || $ok->{$xlabel};
    $stone->insert(_canonicalize($xlabel),$value);
}

#<LIGT>
# Following is entirely rewritten
#</LIGT>
sub _addFeaturesToStone {
	my($self,$features,$basecount,$stone,$ok) = @_;
	my($f) = new Stone;
	foreach (@$features) {
		my($q) = $_->{'value'};
		my($label) = _canonicalize($_->{'label'});
		my($position) = $q=~m!^([^/]+)!;
		my @qualifiers = $q=~m!/(\w+)=([^/]+)!g;
		my %qualifiers;
		while (my($key,$value) = splice(@qualifiers,0,2)) {
			$value =~ s/^\s*\"//;
			$value =~s/\"\s*$//;
			$value=~s/\s+//g if uc($key) eq 'TRANSLATION';  
			$qualifiers{_canonicalize($key)} = $value;
		}
		$f->insert($label=>new Stone('Position'=>$position,%qualifiers));
	}
	$stone->insert('Features',$f);
}



# -------------------------- DEFINITION OF ACCESSOR OBJECTS ------------------------------
#<LIGT>
#only name changes for avoid namespace collisions
#</LIGT>
package UnigeneAccessor;
use Carp;

sub new {
    my($class,@parameters) = @_;
    croak "UnigeneAccessor::new:  Abstract class\n";
}

sub fetch_next {
    my($self) = @_;
    croak "UnigeneAccessor::fetch_next: Abstract class\n";
}

sub DESTROY {
}

#<LIGT>
# Following, only the File package since the only one supported.
# If other access methods must be supported, then here appropriate
# packages and methods must be implemented
#</LIGT>
package File;
use Carp;
@ISA=qw(UnigeneAccessor);
$DEFAULT_PATH = Boulder::Unigene::DEFAULT_UNIGENE_PATH();

#<LIGT>
# Following, removed the search for the string locus in the file
#   as validation that the input be compliant with parser
#</LIGT>
sub new {
    my($package,$path) = @_;
    $path = $DEFAULT_PATH unless $path;
    open (UG,$path) or croak "File::new(): couldn't open $path: $!";
    # read the junk at the beginning
    my $found; $found++;
    croak "File::new(): $path doesn't look like a Unigene flat file"
	unless $found;
    $_ = <UG>;
    return bless {'fh'=>UG},$package;
}

#<LIGT>
# Following, changed the record separator
#</LIGT>
sub fetch_next {
    my $self = shift;
    return undef unless $self->{'fh'};
    local($/)="//\n";
    my($line);
    my($fh) = $self->{'fh'};
    chomp($line = <$fh>);
    return $line;
}

1;

__END__