ensembl-hive  2.7.0
VBCoordinateMapper.pm
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2 
3 See the NOTICE file distributed with this work for additional information
4 regarding copyright ownership.
5 
6 Licensed under the Apache License, Version 2.0 (the "License");
7 you may not use this file except in compliance with the License.
8 You may obtain a copy of the License at
9 
10  http://www.apache.org/licenses/LICENSE-2.0
11 
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13 distributed under the License is distributed on an "AS IS" BASIS,
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15 See the License for the specific language governing permissions and
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18 =cut
19 
20 # $Id$
21 
22 # This is a set of subroutines used for creating Xrefs based on
23 # coordinate overlaps.
24 
25 package XrefMapper::VBCoordinateMapper;
26 
27 use strict;
28 use warnings;
29 
30 use Bio::EnsEMBL::DBSQL::DBAdaptor;
31 use Bio::EnsEMBL::Mapper::RangeRegistry;
32 
33 use Carp;
34 use IO::File;
35 use File::Spec::Functions;
36 
37 use vars '@ISA';
38 
39 @ISA = qw{ XrefMapper::CoordinateMapper };
40 
41 
42 our @EXPORT = qw( run_coordinatemapping );
43 
44 our $coding_weight = 2;
45 our $ens_weight = 3;
46 
47 our $transcript_score_threshold = 0.75;
48 
49 sub run_coordinatemapping {
50  print STDERR "RUNNING VB COORD MAPPING\n";
51  my ( $mapper, $do_upload ) = @_;
52 
53  my $xref_db = $mapper->xref();
54  my $core_db = $mapper->core();
55 
56  my $species = $core_db->species();
57  my $species_id =
58  XrefMapper::BasicMapper::get_species_id_from_species_name( $xref_db,
59  $species );
60 
61  # We only do coordinate mapping for mouse and human for now.
62  if ( !( $species eq 'mus_musculus' || $species eq 'homo_sapiens' ) ) {
63 # return;
64  }
65 
66  my $output_dir = $core_db->dir();
67 
68  my $xref_filename = catfile( $output_dir, 'xref_coord.txt' );
69  my $object_xref_filename =
70  catfile( $output_dir, 'object_xref_coord.txt' );
71  my $unmapped_reason_filename =
72  catfile( $output_dir, 'unmapped_reason_coord.txt' );
73  my $unmapped_object_filename =
74  catfile( $output_dir, 'unmapped_object_coord.txt' );
75 
76  my $xref_dbh = $xref_db->dbc()->db_handle();
77  my $core_dbh = $core_db->dbc()->db_handle();
78 
79  ######################################################################
80  # Figure out the last used 'xref_id', 'object_xref_id', #
81  # 'unmapped_object_id', and 'unmapped_reason_id' from the Core #
82  # database. #
83  ######################################################################
84 
85  my $xref_id =
86  $core_dbh->selectall_arrayref('SELECT MAX(xref_id) FROM xref')
87  ->[0][0];
88  my $object_xref_id = $core_dbh->selectall_arrayref(
89  'SELECT MAX(object_xref_id) FROM object_xref')->[0][0];
90  my $unmapped_object_id = $core_dbh->selectall_arrayref(
91  'SELECT MAX(unmapped_object_id) FROM unmapped_object')->[0][0];
92  my $unmapped_reason_id = $core_dbh->selectall_arrayref(
93  'SELECT MAX(unmapped_reason_id) FROM unmapped_reason')->[0][0];
94 
95  log_progress( "Last used xref_id is %d\n", $xref_id );
96  log_progress( "Last used object_xref_id is %d\n",
97  $object_xref_id );
98  log_progress( "Last used unmapped_object_id is %d\n",
99  $unmapped_object_id );
100  log_progress( "Last used unmapped_reason_id is %d\n",
101  $unmapped_reason_id );
102 
103  ######################################################################
104  # Get an 'analysis_id', or discover that we need to add our analysis #
105  # to the 'analyis' table later. #
106  ######################################################################
107 
108  my $analysis_params =
109  sprintf( "weights(coding,ensembl)="
110  . "%.2f,%.2f;"
111  . "transcript_score_threshold=" . "%.2f",
112  $coding_weight, $ens_weight, $transcript_score_threshold );
113 
114  my $analysis_sql = qq(
115  SELECT analysis_id
116  FROM analysis
117  WHERE logic_name = 'xrefcoordinatemapping'
118  AND parameters = ?
119  );
120 
121  my $analysis_sth = $core_dbh->prepare($analysis_sql);
122  $analysis_sth->execute($analysis_params);
123 
124  my $analysis_id = $analysis_sth->fetchall_arrayref()->[0][0];
125  if ( !defined($analysis_id) ) {
126  $analysis_id =
127  $core_dbh->selectall_arrayref( "SELECT analysis_id FROM analysis "
128  . "WHERE logic_name = 'xrefcoordinatemapping'" )->[0][0];
129 
130  if ( defined($analysis_id) && $do_upload ) {
131  log_progress( "Will update 'analysis' table "
132  . "with new parameter settings\n" );
133 
134  #-----------------------------------------------------------------
135  # Update an existing analysis.
136  #-----------------------------------------------------------------
137 
138  my $sql = qq(
139  UPDATE analysis
140  SET created = now(), parameters = ?
141  WHERE analysis_id = ?
142  );
143 
144  $core_dbh->do( $sql, undef, $analysis_params, $analysis_id );
145 
146  } else {
147  log_progress("Can not find analysis ID for this analysis:\n");
148  log_progress(" logic_name = 'xrefcoordinatemapping'\n");
149  log_progress( " parameters = '%s'\n", $analysis_params );
150 
151  if ($do_upload) {
152  #---------------------------------------------------------------
153  # Store a new analysis.
154  #---------------------------------------------------------------
155 
156  log_progress("A new analysis will be added\n");
157 
158  $analysis_id = $core_dbh->selectall_arrayref(
159  'SELECT MAX(analysis_id) FROM analysis')->[0][0];
160  log_progress( "Last used analysis_id is %d\n", $analysis_id );
161 
162  my $sql = 'INSERT INTO analysis '
163  . 'VALUES(?, now(), ?, \N, \N, \N, ?, \N, \N, ?, ?, \N, \N, \N)';
164  my $sth = $core_dbh->prepare($sql);
165 
166  $sth->execute( ++$analysis_id, 'xrefcoordinatemapping',
167  'CoordinateMapper.pm', $analysis_params,
168  'CoordinateMapper.pm' );
169  }
170  } ## end else [ if ( defined($analysis_id...
171  } ## end if ( !defined($analysis_id...
172 
173  if ( defined($analysis_id) ) {
174  log_progress( "Analysis ID is %d\n",
175  $analysis_id );
176  }
177 
178  ######################################################################
179  # Read and store available Xrefs from the Xref database. #
180  ######################################################################
181 
182  my %unmapped;
183  my %mapped;
184 
185  my $xref_sql = qq(
186  SELECT coord_xref_id, source_id, accession
187  FROM coordinate_xref
188  WHERE species_id = ?
189  );
190 
191  my $xref_sth = $xref_dbh->prepare($xref_sql);
192  $xref_sth->execute($species_id);
193 
194  while ( my $xref = $xref_sth->fetchrow_hashref() ) {
195  $unmapped{ $xref->{'coord_xref_id'} } = {
196  'external_db_id' =>
197  $XrefMapper::BasicMapper::source_to_external_db{ $xref->{
198  'source_id'} }
199  || 11000, # FIXME (11000 is 'UCSC')
200  'accession' => $xref->{'accession'},
201  'reason' => 'No overlap',
202  'reason_full' =>
203  'No coordinate overlap with any Ensembl transcript' };
204  }
205  $xref_sth->finish();
206 
207  ######################################################################
208  # Do coordinate matching. #
209  ######################################################################
210 
211  my $core_db_adaptor =
212  Bio::EnsEMBL::DBSQL::DBAdaptor->new(
213  -host => $core_db->dbc()->host(),
214  -port => $core_db->dbc()->port(),
215  -user => $core_db->dbc()->username(),
216  -pass => $core_db->dbc()->password(),
217  -dbname => $core_db->dbc()->dbname(),
218  );
219 
220  my $slice_adaptor = $core_db_adaptor->get_SliceAdaptor();
221  my @chromosomes = @{ $slice_adaptor->fetch_all('Chromosome') };
222 
223  my $sql = qq(
224  SELECT coord_xref_id, accession,
225  txStart, txEnd,
226  cdsStart, cdsEnd,
227  exonStarts, exonEnds
228  FROM coordinate_xref
229  WHERE species_id = ?
230  AND chromosome = ? AND strand = ?
231  AND ((txStart >= ? AND txStart <= ?) -- txStart in region
232  OR (txEnd >= ? AND txEnd <= ?) -- txEnd in region
233  OR (txStart <= ? AND txEnd >= ?)) -- region is contained
234  ORDER BY accession
235  );
236 
237  foreach my $chromosome (@chromosomes) {
238  my $chr_name = $chromosome->seq_region_name();
239 
240  log_progress( "Processing chromsome '%s'\n", $chr_name );
241 
242  my @genes = @{ $chromosome->get_all_Genes( undef, undef, 1 ) };
243 
244  log_progress( "There are %4d genes on chromosome '%s'\n",
245  scalar(@genes), $chr_name );
246 
247  while ( my $gene = shift(@genes) ) {
248  my @transcripts = @{ $gene->get_all_Transcripts() };
249 
250  my %gene_result;
251 
252  foreach my $transcript ( sort { $a->start() <=> $b->start() }
253  @transcripts )
254  {
255  ################################################################
256  # For each Ensembl transcript: #
257  # 1. Register all Ensembl exons in a RangeRegistry. #
258  # #
259  # 2. Find all transcripts in the external database that are #
260  # within the range of this Ensembl transcript. #
261  # #
262  # For each of those external transcripts: #
263  # 3. Calculate the overlap of the exons of the external #
264  # transcript with the Ensembl exons using the #
265  # overlap_size() method in the RangeRegistry. #
266  # #
267  # 4. Register the external exons in their own RangeRegistry. #
268  # #
269  # 5. Calculate the overlap of the Ensembl exons with the #
270  # external exons as in step 3. #
271  # #
272  # 6. Calculate the match score. #
273  # #
274  # 7. Decide whether or not to keep the match. #
275  ################################################################
276 
277  my @exons = @{ $transcript->get_all_Exons() };
278 
279  my %transcript_result;
280 
281  # '$rr1' is the RangeRegistry holding Ensembl exons for one
282  # transcript at a time.
283  my $rr1 = Bio::EnsEMBL::Mapper::RangeRegistry->new();
284 
285  my $coding_transcript;
286  if ( defined( $transcript->translation() ) ) {
287  $coding_transcript = 1;
288  } else {
289  $coding_transcript = 0;
290  }
291 
292  foreach my $exon (@exons) {
293  #-------------------------------------------------------------
294  # Register each exon in the RangeRegistry. Register both the
295  # total length of the exon and the coding range of the exon.
296  #-------------------------------------------------------------
297 
298  $rr1->check_and_register( 'exon', $exon->start(),
299  $exon->end() );
300 
301  if ( $coding_transcript
302  && defined( $exon->coding_region_start($transcript) )
303  && defined( $exon->coding_region_end($transcript) ) )
304  {
305  $rr1->check_and_register(
306  'coding',
307  $exon->coding_region_start($transcript),
308  $exon->coding_region_end($transcript) );
309  }
310  }
311 
312  #---------------------------------------------------------------
313  # Get hold of all transcripts from the external database that
314  # overlaps with this Ensembl transcript.
315  #---------------------------------------------------------------
316 
317  my $sth = $xref_dbh->prepare_cached($sql);
318  $sth->execute( $species_id, $chr_name,
319  $gene->strand(), $transcript->start(),
320  $transcript->end(), $transcript->start(),
321  $transcript->end(), $transcript->start(),
322  $transcript->end() );
323 
324  my ( $coord_xref_id, $accession, $txStart, $txEnd, $cdsStart,
325  $cdsEnd, $exonStarts, $exonEnds );
326 
327  $sth->bind_columns(
328  \( $coord_xref_id, $accession, $txStart, $txEnd,
329  $cdsStart, $cdsEnd, $exonStarts, $exonEnds
330  ) );
331 
332  while ( $sth->fetch() ) {
333  my @exonStarts = split( /,\s*/, $exonStarts );
334  my @exonEnds = split( /,\s*/, $exonEnds );
335  my $exonCount = scalar(@exonStarts);
336 
337  # '$rr2' is the RangeRegistry holding exons from the external
338  # transcript, for one transcript at a time.
339  my $rr2 = Bio::EnsEMBL::Mapper::RangeRegistry->new();
340 
341  my $exon_match = 0;
342  my $coding_match = 0;
343 
344  my $coding_count = 0;
345 
346  for ( my $i = 0 ; $i < $exonCount ; ++$i ) {
347  #-----------------------------------------------------------
348  # Register the exons from the external database in the same
349  # was as with the Ensembl exons, and calculate the overlap
350  # of the external exons with the previously registered
351  # Ensembl exons.
352  #-----------------------------------------------------------
353 
354  my $overlap =
355  $rr1->overlap_size( 'exon', $exonStarts[$i],
356  $exonEnds[$i] );
357 
358  $exon_match +=
359  $overlap/( $exonEnds[$i] - $exonStarts[$i] + 1 );
360 
361  $rr2->check_and_register( 'exon', $exonStarts[$i],
362  $exonEnds[$i] );
363 
364  if ( !defined($cdsStart) || !defined($cdsEnd) ) {
365  # Non-coding transcript.
366  } else {
367  my $codingStart = ( $exonStarts[$i] > $cdsStart
368  ? $exonStarts[$i]
369  : $cdsStart );
370  my $codingEnd =
371  ( $exonEnds[$i] < $cdsEnd ? $exonEnds[$i] : $cdsEnd );
372 
373  if ( $codingStart < $codingEnd ) {
374  my $coding_overlap =
375  $rr1->overlap_size( 'coding', $codingStart,
376  $codingEnd );
377 
378  $coding_match +=
379  $coding_overlap/( $codingEnd - $codingStart + 1 );
380 
381  $rr2->check_and_register( 'coding', $codingStart,
382  $codingEnd );
383 
384  ++$coding_count;
385  }
386  }
387  } ## end for ( my $i = 0 ; $i < ...
388 
389  my $rexon_match = 0;
390  my $rcoding_match = 0;
391 
392  my $rcoding_count = 0;
393 
394  foreach my $exon (@exons) {
395  #-----------------------------------------------------------
396  # Calculate the overlap of the Ensembl exons with the
397  # external exons.
398  #-----------------------------------------------------------
399 
400  my $overlap =
401  $rr2->overlap_size( 'exon', $exon->start(),
402  $exon->end() );
403 
404  $rexon_match +=
405  $overlap/( $exon->end() - $exon->start() + 1 );
406 
407  if ( $coding_transcript
408  && defined( $exon->coding_region_start($transcript) )
409  && defined( $exon->coding_region_end($transcript) ) )
410  {
411  my $coding_overlap =
412  $rr2->overlap_size( 'coding',
413  $exon->coding_region_start(
414  $transcript),
415  $exon->coding_region_end(
416  $transcript)
417  );
418 
419  $rcoding_match +=
420  $coding_overlap/
421  ( $exon->coding_region_end($transcript) -
422  $exon->coding_region_start($transcript) +
423  1 );
424 
425  ++$rcoding_count;
426  }
427  } ## end foreach my $exon (@exons)
428 
429  #-------------------------------------------------------------
430  # Calculate the match score.
431  #-------------------------------------------------------------
432 
433  my $score = ( ( $exon_match + $ens_weight*$rexon_match ) +
434  $coding_weight*(
435  $coding_match + $ens_weight*$rcoding_match
436  )
437  )/( ( $exonCount + $ens_weight*scalar(@exons) ) +
438  $coding_weight*(
439  $coding_count + $ens_weight*$rcoding_count
440  ) );
441 
442  if ( !defined( $transcript_result{$coord_xref_id} )
443  || $transcript_result{$coord_xref_id} < $score )
444  {
445  $transcript_result{$coord_xref_id} = $score;
446  }
447 
448  } ## end while ( $sth->fetch() )
449  $sth->finish();
450 
451  #---------------------------------------------------------------
452  # Apply transcript threshold and pick the best match(es) for
453  # this transcript.
454  #---------------------------------------------------------------
455 
456  my $best_score;
457  foreach my $coord_xref_id (
458  sort( { $transcript_result{$b} <=> $transcript_result{$a} }
459  keys(%transcript_result) ) )
460  {
461 # my $score = $transcript_result{$coord_xref_id};
462 #
463 # if ( $score > $transcript_score_threshold ) {
464 # $best_score ||= $score;
465 #
466 # if ( sprintf( "%.3f", $score ) eq
467 # sprintf( "%.3f", $best_score ) )
468 # {
469  if ( exists( $unmapped{$coord_xref_id} ) ) {
470  $mapped{$coord_xref_id} = $unmapped{$coord_xref_id};
471  delete( $unmapped{$coord_xref_id} );
472  $mapped{$coord_xref_id}{'reason'} = undef;
473  $mapped{$coord_xref_id}{'reason_full'} = undef;
474  }
475 
476  push( @{ $mapped{$coord_xref_id}{'mapped_to'} }, {
477  'ensembl_id' => $transcript->dbID(),
478  'ensembl_object_type' => 'Transcript'
479  } );
480 
481 # # This is now a candidate Xref for the gene.
482 # if ( !defined( $gene_result{$coord_xref_id} )
483 # || $gene_result{$coord_xref_id} < $score )
484 # {
485 # $gene_result{$coord_xref_id} = $score;
486 # }
487 #
488 # } elsif ( exists( $unmapped{$coord_xref_id} ) ) {
489 # $unmapped{$coord_xref_id}{'reason'} =
490 # 'Was not best match';
491 # $unmapped{$coord_xref_id}{'reason_full'} =
492 # sprintf(
493 # "Did not top best transcript match score (%.2f)",
494 # $best_score );
495 # if ( !defined( $unmapped{$coord_xref_id}{'score'} )
496 # || $score > $unmapped{$coord_xref_id}{'score'} )
497 # {
498 # $unmapped{$coord_xref_id}{'score'} = $score;
499 # $unmapped{$coord_xref_id}{'ensembl_id'} =
500 # $transcript->dbID();
501 # }
502 # }
503 #
504 # } elsif ( exists( $unmapped{$coord_xref_id} )
505 # && $unmapped{$coord_xref_id}{'reason'} ne
506 # 'Was not best match' )
507 # {
508 # $unmapped{$coord_xref_id}{'reason'} =
509 # 'Did not meet threshold';
510 # $unmapped{$coord_xref_id}{'reason_full'} =
511 # sprintf( "Match score for transcript "
512 # . "lower than threshold (%.2f)",
513 # $transcript_score_threshold );
514 # if ( !defined( $unmapped{$coord_xref_id}{'score'} )
515 # || $score > $unmapped{$coord_xref_id}{'score'} )
516 # {
517 # $unmapped{$coord_xref_id}{'score'} = $score;
518 # $unmapped{$coord_xref_id}{'ensembl_id'} =
519 # $transcript->dbID();
520 # }
521 # }
522  } ## end foreach my $coord_xref_id (...
523 
524  } ## end foreach my $transcript ( sort...
525 
526  #-----------------------------------------------------------------
527  # Pick the best match(es) for this gene.
528  #-----------------------------------------------------------------
529 
530  my $best_score;
531  foreach my $coord_xref_id (
532  sort( { $gene_result{$b} <=> $gene_result{$a} }
533  keys(%gene_result) ) )
534  {
535 # my $score = $gene_result{$coord_xref_id};
536 #
537 # $best_score ||= $score;
538 #
539 # if (
540 # sprintf( "%.3f", $score ) eq sprintf( "%.3f", $best_score ) )
541 # {
542  push( @{ $mapped{$coord_xref_id}{'mapped_to'} }, {
543  'ensembl_id' => $gene->dbID(),
544  'ensembl_object_type' => 'Gene'
545  } );
546 # }
547  }
548 
549  } ## end while ( my $gene = shift(...
550  } ## end foreach my $chromosome (@chromosomes)
551 
552  # Make all dumps. Order is important.
553  dump_xref( $xref_filename, $xref_id, \%mapped, \%unmapped );
554  dump_object_xref( $object_xref_filename, $object_xref_id, \%mapped );
555  dump_unmapped_reason( $unmapped_reason_filename, $unmapped_reason_id,
556  \%unmapped );
557  dump_unmapped_object( $unmapped_object_filename, $unmapped_object_id,
558  $analysis_id, \%unmapped );
559 
560  if ($do_upload) {
561  upload_data( 'xref', $xref_filename, $core_dbh );
562  upload_data( 'object_xref', $object_xref_filename, $core_dbh );
563  upload_data( 'unmapped_reason', $unmapped_reason_filename,
564  $core_dbh );
565  upload_data( 'unmapped_object', $unmapped_object_filename,
566  $core_dbh );
567  }
568 
569 } ## end sub run_coordinatemapping
570 
571 #-----------------------------------------------------------------------
572 #-----------------------------------------------------------------------
573 
574 sub dump_xref {
575  my ( $filename, $xref_id, $mapped, $unmapped ) = @_;
576 
577  ######################################################################
578  # Dump for 'xref'. #
579  ######################################################################
580 
581  my $fh = IO::File->new( '>' . $filename )
582  or croak( sprintf( "Can not open '%s' for writing", $filename ) );
583 
584  log_progress( "Dumping for 'xref' to '%s'\n", $filename );
585 
586  foreach my $xref ( values( %{$unmapped} ), values( %{$mapped} ) ) {
587  # Assign 'xref_id' to this Xref.
588  $xref->{'xref_id'} = ++$xref_id;
589 
590  my $accession = $xref->{'accession'};
591 
592  my ($version) = ( $accession =~ /\.(\d+)$/ );
593  $version ||= 0;
594 
595  $fh->printf("%d\t%d\t%s\t%s\t%d\t%s\t%s\t%s\n",
596  $xref->{'xref_id'},
597  $xref->{'external_db_id'},
598  $accession,
599  $accession,
600  $version,
601  '\N',
602  'COORDINATE_OVERLAP',
603  '\N' # FIXME (possibly)
604  );
605  }
606  $fh->close();
607 
608  log_progress("Dumping for 'xref' done\n");
609 
610 } ## end sub dump_xref
611 
612 #-----------------------------------------------------------------------
613 
614 sub dump_object_xref {
615  my ( $filename, $object_xref_id, $mapped ) = @_;
616 
617  ######################################################################
618  # Dump for 'object_xref'. #
619  ######################################################################
620 
621  my $fh = IO::File->new( '>' . $filename )
622  or croak( sprintf( "Can not open '%s' for writing", $filename ) );
623 
624  log_progress( "Dumping for 'object_xref' to '%s'\n", $filename );
625 
626  foreach my $xref ( values( %{$mapped} ) ) {
627  foreach my $object_xref ( @{ $xref->{'mapped_to'} } ) {
628  # Assign 'object_xref_id' to this Object Xref.
629  $object_xref->{'object_xref_id'} = ++$object_xref_id;
630 
631  $fh->printf( "%d\t%d\t%s\t%d\t%s\n",
632  $object_xref->{'object_xref_id'},
633  $object_xref->{'ensembl_id'},
634  $object_xref->{'ensembl_object_type'},
635  $xref->{'xref_id'},
636  '\N' );
637  }
638  }
639  $fh->close();
640 
641  log_progress("Dumping for 'object_xref' done\n");
642 
643 } ## end sub dump_objexref
644 
645 #-----------------------------------------------------------------------
646 
647 sub dump_unmapped_reason {
648  my ( $filename, $unmapped_reason_id, $unmapped ) = @_;
649 
650  ######################################################################
651  # Dump for 'unmapped_reason'. #
652  ######################################################################
653 
654  # Create a list of the unique reasons.
655  my %reasons;
656 
657  foreach my $xref ( values( %{$unmapped} ) ) {
658  if ( !exists( $reasons{ $xref->{'reason_full'} } ) ) {
659  $reasons{ $xref->{'reason_full'} } = {
660  'summary' => $xref->{'reason'},
661  'full' => $xref->{'reason_full'}
662  };
663  }
664  }
665 
666  my $fh = IO::File->new( '>' . $filename )
667  or croak( sprintf( "Can not open '%s' for writing", $filename ) );
668 
669  log_progress( "Dumping for 'unmapped_reason' to '%s'\n", $filename );
670 
671  foreach my $reason (
672  sort( { $a->{'full'} cmp $b->{'full'} } values(%reasons) ) )
673  {
674  # Assign 'unmapped_reason_id' to this reason.
675  $reason->{'unmapped_reason_id'} = ++$unmapped_reason_id;
676 
677  $fh->printf( "%d\t%s\t%s\n", $reason->{'unmapped_reason_id'},
678  $reason->{'summary'}, $reason->{'full'} );
679 
680  }
681  $fh->close();
682 
683  log_progress("Dumping for 'unmapped_reason' done\n");
684 
685  # Assign reasons to the unmapped Xrefs from %reasons.
686  foreach my $xref ( values( %{$unmapped} ) ) {
687  $xref->{'reason'} = $reasons{ $xref->{'reason_full'} };
688  $xref->{'reason_full'} = undef;
689  }
690 
691 } ## end sub dump_unmapped_reason
692 
693 #-----------------------------------------------------------------------
694 
695 sub dump_unmapped_object {
696  my ( $filename, $unmapped_object_id, $analysis_id, $unmapped ) = @_;
697 
698  ######################################################################
699  # Dump for 'unmapped_object'. #
700  ######################################################################
701 
702  my $fh = IO::File->new( '>' . $filename )
703  or croak( sprintf( "Can not open '%s' for writing", $filename ) );
704 
705  log_progress( "Dumping for 'unmapped_object' to '%s'\n", $filename );
706 
707  foreach my $xref ( values( %{$unmapped} ) ) {
708  # Assign 'unmapped_object_id' to this Xref.
709  $xref->{'unmapped_object_id'} = ++$unmapped_object_id;
710 
711  $fh->printf(
712  "%d\t%s\t%s\t%d\t%s\t%d\t%s\t%s\t%s\t%s\t%s\n",
713  $xref->{'unmapped_object_id'},
714  'xref',
715  $analysis_id || '\N', # '\N' (NULL) means no analysis exists
716  # and uploading this table will fail.
717  $xref->{'external_db_id'},
718  $xref->{'accession'},
719  $xref->{'reason'}->{'unmapped_reason_id'}, (
720  defined( $xref->{'score'} )
721  ? sprintf( "%.3f", $xref->{'score'} )
722  : '\N'
723  ),
724  '\N',
725  $xref->{'ensembl_id'} || '\N',
726  ( defined( $xref->{'ensembl_id'} ) ? 'Transcript' : '\N' ),
727  '\N' );
728  }
729  $fh->close();
730 
731  log_progress("Dumping for 'unmapped_object' done\n");
732 
733 } ## end sub dump_unmapped_object
734 
735 #-----------------------------------------------------------------------
736 
737 sub upload_data {
738  my ( $table_name, $filename, $dbh ) = @_;
739 
740  ######################################################################
741  # Upload data from a file to a table. #
742  ######################################################################
743 
744  if ( !-r $filename ) {
745  croak( sprintf( "Can not open '%s' for reading", $filename ) );
746  }
747 
748  log_progress( "Uploading for '%s' from '%s'\n",
749  $table_name, $filename );
750 
751  my $sql =
752  sprintf( "LOAD DATA LOCAL INFILE ? REPLACE INTO TABLE %s", $table_name );
753 
754  my $sth = $dbh->prepare($sql);
755 
756  $sth->execute($filename);
757 
758  log_progress( "Uploading for '%s' done\n", $table_name );
759 
760 } ## end sub upload_data
761 
762 #-----------------------------------------------------------------------
763 
764 sub log_progress {
765  my ( $fmt, @params ) = @_;
766  printf( STDERR "COORD==> %s", sprintf( $fmt, @params ) );
767 }
768 
769 1;
Bio::EnsEMBL::Mapper::RangeRegistry
Definition: RangeRegistry.pm:51
Bio::EnsEMBL::DBSQL::DBAdaptor
Definition: DBAdaptor.pm:40
accession
public accession()
XrefMapper::CoordinateMapper
Definition: CoordinateMapper.pm:8
Bio::EnsEMBL::Mapper::RangeRegistry::overlap_size
public Int overlap_size()
Bio::EnsEMBL::DBSQL::DBAdaptor::new
public Bio::EnsEMBL::DBSQL::DBAdaptor new()
XrefMapper::BasicMapper::get_species_id_from_species_name
public get_species_id_from_species_name()
Bio::EnsEMBL::Mapper::RangeRegistry::new
public Bio::EnsEMBL::Mapper::RangeRegistry new()
Bio::EnsEMBL::Mapper::RangeRegistry::check_and_register
public Undef check_and_register()