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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ext.ensembl

File EnsemblSeqProxy.java

 

Coverage histogram

../../../img/srcFileCovDistChart2.png
50% of files have more coverage

Code metrics

100
221
25
2
972
521
87
0.39
8.84
12.5
3.48

Classes

Class Line # Actions
EnsemblSeqProxy 61 219 85
0.1900584819%
EnsemblSeqProxy.EnsemblSeqType 68 2 2
0.00%
 

Contributing tests

This file is covered by 27 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.ext.ensembl;
22   
23    import java.io.IOException;
24    import java.net.MalformedURLException;
25    import java.net.URL;
26    import java.util.ArrayList;
27    import java.util.Arrays;
28    import java.util.Collections;
29    import java.util.List;
30    import java.util.Map;
31   
32    import org.json.simple.parser.ParseException;
33   
34    import jalview.analysis.AlignmentUtils;
35    import jalview.analysis.Dna;
36    import jalview.bin.Cache;
37    import jalview.datamodel.Alignment;
38    import jalview.datamodel.AlignmentI;
39    import jalview.datamodel.DBRefEntry;
40    import jalview.datamodel.DBRefSource;
41    import jalview.datamodel.Mapping;
42    import jalview.datamodel.Sequence;
43    import jalview.datamodel.SequenceFeature;
44    import jalview.datamodel.SequenceI;
45    import jalview.datamodel.features.SequenceFeatures;
46    import jalview.exceptions.JalviewException;
47    import jalview.io.gff.Gff3Helper;
48    import jalview.io.gff.SequenceOntologyFactory;
49    import jalview.io.gff.SequenceOntologyI;
50    import jalview.util.Comparison;
51    import jalview.util.DBRefUtils;
52    import jalview.util.IntRangeComparator;
53    import jalview.util.MapList;
54   
55    /**
56    * Base class for Ensembl sequence fetchers
57    *
58    * @see http://rest.ensembl.org/documentation/info/sequence_id
59    * @author gmcarstairs
60    */
 
61    public abstract class EnsemblSeqProxy extends EnsemblRestClient
62    {
63    protected static final String DESCRIPTION = "description";
64   
65    /*
66    * enum for 'type' parameter to the /sequence REST service
67    */
 
68    public enum EnsemblSeqType
69    {
70    /**
71    * type=genomic to fetch full dna including introns
72    */
73    GENOMIC("genomic"),
74   
75    /**
76    * type=cdna to fetch coding dna including UTRs
77    */
78    CDNA("cdna"),
79   
80    /**
81    * type=cds to fetch coding dna excluding UTRs
82    */
83    CDS("cds"),
84   
85    /**
86    * type=protein to fetch peptide product sequence
87    */
88    PROTEIN("protein");
89   
90    /*
91    * the value of the 'type' parameter to fetch this version of
92    * an Ensembl sequence
93    */
94    private String type;
95   
 
96  0 toggle EnsemblSeqType(String t)
97    {
98  0 type = t;
99    }
100   
 
101  0 toggle public String getType()
102    {
103  0 return type;
104    }
105   
106    }
107   
108    /**
109    * Default constructor (to use rest.ensembl.org)
110    */
 
111  32 toggle public EnsemblSeqProxy()
112    {
113  32 super();
114    }
115   
116    /**
117    * Constructor given the target domain to fetch data from
118    */
 
119  0 toggle public EnsemblSeqProxy(String d)
120    {
121  0 super(d);
122    }
123   
124    /**
125    * Makes the sequence queries to Ensembl's REST service and returns an
126    * alignment consisting of the returned sequences.
127    */
 
128  0 toggle @Override
129    public AlignmentI getSequenceRecords(String query) throws Exception
130    {
131    // TODO use a String... query vararg instead?
132   
133    // danger: accession separator used as a regex here, a string elsewhere
134    // in this case it is ok (it is just a space), but (e.g.) '\' would not be
135  0 List<String> allIds = Arrays
136    .asList(query.split(getAccessionSeparator()));
137  0 AlignmentI alignment = null;
138  0 inProgress = true;
139   
140    /*
141    * execute queries, if necessary in batches of the
142    * maximum allowed number of ids
143    */
144  0 int maxQueryCount = getMaximumQueryCount();
145  0 for (int v = 0, vSize = allIds.size(); v < vSize; v += maxQueryCount)
146    {
147  0 int p = Math.min(vSize, v + maxQueryCount);
148  0 List<String> ids = allIds.subList(v, p);
149  0 try
150    {
151  0 alignment = fetchSequences(ids, alignment);
152    } catch (Throwable r)
153    {
154  0 inProgress = false;
155  0 String msg = "Aborting ID retrieval after " + v
156    + " chunks. Unexpected problem (" + r.getLocalizedMessage()
157    + ")";
158  0 System.err.println(msg);
159  0 r.printStackTrace();
160  0 break;
161    }
162    }
163   
164  0 if (alignment == null)
165    {
166  0 return null;
167    }
168   
169    /*
170    * fetch and transfer genomic sequence features,
171    * fetch protein product and add as cross-reference
172    */
173  0 for (int i = 0, n = allIds.size(); i < n; i++)
174    {
175  0 addFeaturesAndProduct(allIds.get(i), alignment);
176    }
177   
178  0 List<SequenceI> seqs = alignment.getSequences();
179  0 for (int i = 0, n = seqs.size(); i < n; i++)
180    {
181  0 getCrossReferences(seqs.get(i));
182    }
183   
184  0 return alignment;
185    }
186   
187    /**
188    * Fetches Ensembl features using the /overlap REST endpoint, and adds them to
189    * the sequence in the alignment. Also fetches the protein product, maps it
190    * from the CDS features of the sequence, and saves it as a cross-reference of
191    * the dna sequence.
192    *
193    * @param accId
194    * @param alignment
195    */
 
196  0 toggle protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
197    {
198  0 if (alignment == null)
199    {
200  0 return;
201    }
202   
203  0 try
204    {
205    /*
206    * get 'dummy' genomic sequence with gene, transcript,
207    * exon, cds and variation features
208    */
209  0 SequenceI genomicSequence = null;
210  0 EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
211  0 EnsemblFeatureType[] features = getFeaturesToFetch();
212   
213    // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);
214   
215  0 AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
216    features);
217  0 if (geneFeatures != null && geneFeatures.getHeight() > 0)
218    {
219  0 genomicSequence = geneFeatures.getSequenceAt(0);
220    }
221   
222    // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);
223   
224  0 if (genomicSequence != null)
225    {
226    /*
227    * transfer features to the query sequence
228    */
229  0 SequenceI querySeq = alignment.findName(accId, true);
230  0 if (transferFeatures(accId, genomicSequence, querySeq))
231    {
232   
233    /*
234    * fetch and map protein product, and add it as a cross-reference
235    * of the retrieved sequence
236    */
237    // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);
238  0 addProteinProduct(querySeq);
239    }
240    }
241    } catch (IOException e)
242    {
243  0 System.err.println(
244    "Error transferring Ensembl features: " + e.getMessage());
245    }
246    // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
247    }
248   
249    /**
250    * Returns those sequence feature types to fetch from Ensembl. We may want
251    * features either because they are of interest to the user, or as means to
252    * identify the locations of the sequence on the genomic sequence (CDS
253    * features identify CDS, exon features identify cDNA etc).
254    *
255    * @return
256    */
257    protected abstract EnsemblFeatureType[] getFeaturesToFetch();
258   
259    /**
260    * Fetches and maps the protein product, and adds it as a cross-reference of
261    * the retrieved sequence
262    */
 
263  0 toggle protected void addProteinProduct(SequenceI querySeq)
264    {
265  0 String accId = querySeq.getName();
266  0 try
267    {
268  0 System.out.println("Adding protein product for " + accId);
269  0 AlignmentI protein = new EnsemblProtein(getDomain())
270    .getSequenceRecords(accId);
271  0 if (protein == null || protein.getHeight() == 0)
272    {
273  0 System.out.println("No protein product found for " + accId);
274  0 return;
275    }
276  0 SequenceI proteinSeq = protein.getSequenceAt(0);
277   
278    /*
279    * need dataset sequences (to be the subject of mappings)
280    */
281  0 proteinSeq.createDatasetSequence();
282  0 querySeq.createDatasetSequence();
283   
284  0 MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq,
285    proteinSeq);
286  0 if (mapList != null)
287    {
288    // clunky: ensure Uniprot xref if we have one is on mapped sequence
289  0 SequenceI ds = proteinSeq.getDatasetSequence();
290    // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence()
291  0 Mapping map = new Mapping(ds, mapList);
292  0 DBRefEntry dbr = new DBRefEntry(getDbSource(),
293    getEnsemblDataVersion(), proteinSeq.getName(), map);
294  0 querySeq.getDatasetSequence().addDBRef(dbr);
295  0 List<DBRefEntry> uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
296    new String[]
297    { DBRefSource.UNIPROT });
298  0 List<DBRefEntry> upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
299    new String[]
300    { DBRefSource.UNIPROT });
301  0 if (uprots != null)
302    {
303  0 for (DBRefEntry up : uprots)
304    {
305    // locate local uniprot ref and map
306  0 List<DBRefEntry> upx = DBRefUtils.searchRefs(upxrefs,
307    up.getAccessionId());
308  0 DBRefEntry upxref;
309  0 if (upx.size() != 0)
310    {
311  0 upxref = upx.get(0);
312   
313  0 if (upx.size() > 1)
314    {
315  0 Cache.log.warn(
316    "Implementation issue - multiple uniprot acc on product sequence.");
317    }
318    }
319    else
320    {
321  0 upxref = new DBRefEntry(DBRefSource.UNIPROT,
322    getEnsemblDataVersion(), up.getAccessionId());
323    }
324   
325  0 Mapping newMap = new Mapping(ds, mapList);
326  0 upxref.setVersion(getEnsemblDataVersion());
327  0 upxref.setMap(newMap);
328  0 if (upx.size() == 0)
329    {
330    // add the new uniprot ref
331  0 querySeq.getDatasetSequence().addDBRef(upxref);
332    }
333   
334    }
335    }
336   
337    /*
338    * copy exon features to protein, compute peptide variants from dna
339    * variants and add as features on the protein sequence ta-da
340    */
341    // JAL-3187 render on the fly instead
342    // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList);
343    }
344    } catch (Exception e)
345    {
346  0 System.err
347    .println(String.format("Error retrieving protein for %s: %s",
348    accId, e.getMessage()));
349    }
350    }
351   
352    /**
353    * Get database xrefs from Ensembl, and attach them to the sequence
354    *
355    * @param seq
356    */
 
357  0 toggle protected void getCrossReferences(SequenceI seq)
358    {
359   
360    // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);
361   
362   
363  0 while (seq.getDatasetSequence() != null)
364    {
365  0 seq = seq.getDatasetSequence();
366    }
367   
368    // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);
369   
370  0 EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
371    getEnsemblDataVersion());
372  0 List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
373   
374  0 for (int i = 0, n = xrefs.size(); i < n; i++)
375    {
376    // Platform.timeCheck("ESP. getxref + " + (i) + "/" + n, Platform.TIME_MARK);
377    // BH 2019.01.25 this next method was taking 174 ms PER addition for a 266-reference example.
378    // DBRefUtils.ensurePrimaries(seq)
379    // was at the end of seq.addDBRef, so executed after ever addition!
380    // This method was moved to seq.getPrimaryDBRefs()
381  0 seq.addDBRef(xrefs.get(i));
382    }
383   
384    // System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
385    /*
386    * and add a reference to itself
387    */
388   
389    // Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);
390   
391  0 DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
392    seq.getName());
393   
394    // Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);
395   
396  0 seq.addDBRef(self);
397   
398    // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);
399    }
400   
401    /**
402    * Fetches sequences for the list of accession ids and adds them to the
403    * alignment. Returns the extended (or created) alignment.
404    *
405    * @param ids
406    * @param alignment
407    * @return
408    * @throws JalviewException
409    * @throws IOException
410    */
 
411  0 toggle protected AlignmentI fetchSequences(List<String> ids,
412    AlignmentI alignment) throws JalviewException, IOException
413    {
414  0 if (!isEnsemblAvailable())
415    {
416  0 inProgress = false;
417  0 throw new JalviewException("ENSEMBL Rest API not available.");
418    }
419    // Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
420   
421  0 List<SequenceI> seqs = parseSequenceJson(ids);
422  0 if (seqs == null)
423  0 return alignment;
424   
425  0 if (seqs.isEmpty())
426    {
427  0 throw new IOException("No data returned for " + ids);
428    }
429   
430  0 if (seqs.size() != ids.size())
431    {
432  0 System.out.println(String.format(
433    "Only retrieved %d sequences for %d query strings",
434    seqs.size(), ids.size()));
435    }
436   
437  0 if (!seqs.isEmpty())
438    {
439  0 AlignmentI seqal = new Alignment(
440    seqs.toArray(new SequenceI[seqs.size()]));
441  0 for (SequenceI seq : seqs)
442    {
443  0 if (seq.getDescription() == null)
444    {
445  0 seq.setDescription(getDbName());
446    }
447  0 String name = seq.getName();
448  0 if (ids.contains(name)
449    || ids.contains(name.replace("ENSP", "ENST")))
450    {
451    // TODO JAL-3077 use true accession version in dbref
452  0 DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(),
453    getEnsemblDataVersion(), name);
454  0 seq.addDBRef(dbref);
455    }
456    }
457  0 if (alignment == null)
458    {
459  0 alignment = seqal;
460    }
461    else
462    {
463  0 alignment.append(seqal);
464    }
465    }
466  0 return alignment;
467    }
468   
469    /**
470    * Parses a JSON response for a single sequence ID query
471    *
472    * @param br
473    * @return a single jalview.datamodel.Sequence
474    * @see http://rest.ensembl.org/documentation/info/sequence_id
475    */
 
476  0 toggle @SuppressWarnings("unchecked")
477    protected List<SequenceI> parseSequenceJson(List<String> ids)
478    {
479  0 List<SequenceI> result = new ArrayList<>();
480  0 try
481    {
482    /*
483    * for now, assumes only one sequence returned; refactor if needed
484    * in future to handle a JSONArray with more than one
485    */
486    // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
487  0 Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
488  0 if (val == null)
489  0 return null;
490  0 Object s = val.get("desc");
491  0 String desc = s == null ? null : s.toString();
492  0 s = val.get("id");
493  0 String id = s == null ? null : s.toString();
494  0 s = val.get("seq");
495  0 String seq = s == null ? null : s.toString();
496  0 Sequence sequence = new Sequence(id, seq);
497  0 if (desc != null)
498    {
499  0 sequence.setDescription(desc);
500    }
501    // todo JAL-3077 make a DBRefEntry with true accession version
502    // s = val.get("version");
503    // String version = s == null ? "0" : s.toString();
504    // DBRefEntry dbref = new DBRefEntry(getDbSource(), version, id);
505    // sequence.addDBRef(dbref);
506  0 result.add(sequence);
507    } catch (ParseException | IOException e)
508    {
509  0 System.err.println("Error processing JSON response: " + e.toString());
510    // ignore
511    }
512    // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
513  0 return result;
514    }
515   
516    /**
517    * Returns the URL for the REST call
518    *
519    * @return
520    * @throws MalformedURLException
521    */
 
522  0 toggle @Override
523    protected URL getUrl(List<String> ids) throws MalformedURLException
524    {
525    /*
526    * a single id is included in the URL path
527    * multiple ids go in the POST body instead
528    */
529  0 StringBuffer urlstring = new StringBuffer(128);
530  0 urlstring.append(getDomain() + "/sequence/id");
531  0 if (ids.size() == 1)
532    {
533  0 urlstring.append("/").append(ids.get(0));
534    }
535    // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
536  0 urlstring.append("?type=").append(getSourceEnsemblType().getType());
537  0 urlstring.append(("&Accept=application/json"));
538  0 urlstring.append(("&content-type=application/json"));
539   
540  0 String objectType = getObjectType();
541  0 if (objectType != null)
542    {
543  0 urlstring.append("&").append(OBJECT_TYPE).append("=")
544    .append(objectType);
545    }
546   
547  0 URL url = new URL(urlstring.toString());
548  0 return url;
549    }
550   
551    /**
552    * Override this method to specify object_type request parameter
553    *
554    * @return
555    */
 
556  0 toggle protected String getObjectType()
557    {
558  0 return null;
559    }
560   
561    /**
562    * A sequence/id POST request currently allows up to 50 queries
563    *
564    * @see http://rest.ensembl.org/documentation/info/sequence_id_post
565    */
 
566  0 toggle @Override
567    public int getMaximumQueryCount()
568    {
569  0 return 50;
570    }
571   
 
572  0 toggle @Override
573    protected boolean useGetRequest()
574    {
575  0 return false;
576    }
577   
578    /**
579    *
580    * @return the configured sequence return type for this source
581    */
582    protected abstract EnsemblSeqType getSourceEnsemblType();
583   
584    /**
585    * Returns a list of [start, end] genomic ranges corresponding to the sequence
586    * being retrieved.
587    *
588    * The correspondence between the frames of reference is made by locating
589    * those features on the genomic sequence which identify the retrieved
590    * sequence. Specifically
591    * <ul>
592    * <li>genomic sequence is identified by "transcript" features with
593    * ID=transcript:transcriptId</li>
594    * <li>cdna sequence is identified by "exon" features with
595    * Parent=transcript:transcriptId</li>
596    * <li>cds sequence is identified by "CDS" features with
597    * Parent=transcript:transcriptId</li>
598    * </ul>
599    *
600    * The returned ranges are sorted to run forwards (for positive strand) or
601    * backwards (for negative strand). Aborts and returns null if both positive
602    * and negative strand are found (this should not normally happen).
603    *
604    * @param sourceSequence
605    * @param accId
606    * @param start
607    * the start position of the sequence we are mapping to
608    * @return
609    */
 
610  7 toggle protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
611    String accId, int start)
612    {
613  7 List<SequenceFeature> sfs = getIdentifyingFeatures(sourceSequence,
614    accId);
615  7 if (sfs.isEmpty())
616    {
617  1 return null;
618    }
619   
620    /*
621    * generously initial size for number of cds regions
622    * (worst case titin Q8WZ42 has c. 313 exons)
623    */
624  6 List<int[]> regions = new ArrayList<>(100);
625  6 int mappedLength = 0;
626  6 int direction = 1; // forward
627  6 boolean directionSet = false;
628   
629  6 for (SequenceFeature sf : sfs)
630    {
631  11 int strand = sf.getStrand();
632  11 strand = strand == 0 ? 1 : strand; // treat unknown as forward
633   
634  11 if (directionSet && strand != direction)
635    {
636    // abort - mix of forward and backward
637  0 System.err
638    .println("Error: forward and backward strand for " + accId);
639  0 return null;
640    }
641  11 direction = strand;
642  11 directionSet = true;
643   
644    /*
645    * add to CDS ranges, semi-sorted forwards/backwards
646    */
647  11 if (strand < 0)
648    {
649  2 regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
650    }
651    else
652    {
653  9 regions.add(new int[] { sf.getBegin(), sf.getEnd() });
654    }
655  11 mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
656    }
657   
658  6 if (regions.isEmpty())
659    {
660  0 System.out.println("Failed to identify target sequence for " + accId
661    + " from genomic features");
662  0 return null;
663    }
664   
665    /*
666    * a final sort is needed since Ensembl returns CDS sorted within source
667    * (havana / ensembl_havana)
668    */
669  6 Collections.sort(regions, direction == 1 ? IntRangeComparator.ASCENDING
670    : IntRangeComparator.DESCENDING);
671   
672  6 List<int[]> to = Arrays
673    .asList(new int[]
674    { start, start + mappedLength - 1 });
675   
676  6 return new MapList(regions, to, 1, 1);
677    }
678   
679    /**
680    * Answers a list of sequence features that mark positions of the genomic
681    * sequence feature which are within the sequence being retrieved. For
682    * example, an 'exon' feature whose parent is the target transcript marks the
683    * cdna positions of the transcript. For a gene sequence, this is trivially
684    * just the 'gene' feature with matching gene id.
685    *
686    * @param seq
687    * @param accId
688    * @return
689    */
690    protected abstract List<SequenceFeature> getIdentifyingFeatures(
691    SequenceI seq, String accId);
692   
693    int bhtest = 0;
694   
695    /**
696    * Transfers the sequence feature to the target sequence, locating its start
697    * and end range based on the mapping. Features which do not overlap the
698    * target sequence are ignored.
699    *
700    * @param sf
701    * @param targetSequence
702    * @param mapping
703    * mapping from the sequence feature's coordinates to the target
704    * sequence
705    * @param forwardStrand
706    */
 
707  0 toggle protected void transferFeature(SequenceFeature sf,
708    SequenceI targetSequence, MapList mapping, boolean forwardStrand)
709    {
710  0 int start = sf.getBegin();
711  0 int end = sf.getEnd();
712  0 int[] mappedRange = mapping.locateInTo(start, end);
713   
714  0 if (mappedRange != null)
715    {
716    // Platform.timeCheck(null, Platform.TIME_SET);
717  0 String group = sf.getFeatureGroup();
718  0 if (".".equals(group))
719    {
720  0 group = getDbSource();
721    }
722  0 int newBegin = Math.min(mappedRange[0], mappedRange[1]);
723  0 int newEnd = Math.max(mappedRange[0], mappedRange[1]);
724    // Platform.timeCheck(null, Platform.TIME_MARK);
725  0 bhtest++;
726    // 280 ms/1000 here:
727  0 SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, group, sf.getScore());
728    // 0.175 ms here:
729  0 targetSequence.addSequenceFeature(copy);
730   
731    /*
732    * for sequence_variant on reverse strand, have to convert the allele
733    * values to their complements
734    */
735  0 if (!forwardStrand && SequenceOntologyFactory.getInstance()
736    .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
737    {
738  0 reverseComplementAlleles(copy);
739    }
740    }
741    }
742   
743    /**
744    * Change the 'alleles' value of a feature by converting to complementary
745    * bases, and also update the feature description to match
746    *
747    * @param sf
748    */
 
749  1 toggle static void reverseComplementAlleles(SequenceFeature sf)
750    {
751  1 final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
752  1 if (alleles == null)
753    {
754  0 return;
755    }
756  1 StringBuilder complement = new StringBuilder(alleles.length());
757  1 for (String allele : alleles.split(","))
758    {
759  5 reverseComplementAllele(complement, allele);
760    }
761  1 String comp = complement.toString();
762  1 sf.setValue(Gff3Helper.ALLELES, comp);
763  1 sf.setDescription(comp);
764    }
765   
766    /**
767    * Makes the 'reverse complement' of the given allele and appends it to the
768    * buffer, after a comma separator if not the first
769    *
770    * @param complement
771    * @param allele
772    */
 
773  13 toggle static void reverseComplementAllele(StringBuilder complement,
774    String allele)
775    {
776  13 if (complement.length() > 0)
777    {
778  10 complement.append(",");
779    }
780   
781    /*
782    * some 'alleles' are actually descriptive terms
783    * e.g. HGMD_MUTATION, PhenCode_variation
784    * - we don't want to 'reverse complement' these
785    */
786  13 if (!Comparison.isNucleotideSequence(allele, true))
787    {
788  3 complement.append(allele);
789    }
790    else
791    {
792  29 for (int i = allele.length() - 1; i >= 0; i--)
793    {
794  19 complement.append(Dna.getComplement(allele.charAt(i)));
795    }
796    }
797    }
798   
799    /**
800    * Transfers features from sourceSequence to targetSequence
801    *
802    * @param accessionId
803    * @param sourceSequence
804    * @param targetSequence
805    * @return true if any features were transferred, else false
806    */
 
807  0 toggle protected boolean transferFeatures(String accessionId,
808    SequenceI sourceSequence, SequenceI targetSequence)
809    {
810  0 if (sourceSequence == null || targetSequence == null)
811    {
812  0 return false;
813    }
814   
815    // long start = System.currentTimeMillis();
816  0 List<SequenceFeature> sfs = sourceSequence.getFeatures()
817    .getPositionalFeatures();
818  0 MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
819    accessionId, targetSequence.getStart());
820  0 if (mapping == null)
821    {
822  0 return false;
823    }
824   
825    // Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);
826   
827  0 boolean result = transferFeatures(sfs, targetSequence, mapping,
828    accessionId);
829    // System.out.println("transferFeatures (" + (sfs.size()) + " --> "
830    // + targetSequence.getFeatures().getFeatureCount(true) + ") to "
831    // + targetSequence.getName() + " took "
832    // + (System.currentTimeMillis() - start) + "ms");
833  0 return result;
834    }
835   
836    /**
837    * Transfer features to the target sequence. The start/end positions are
838    * converted using the mapping. Features which do not overlap are ignored.
839    * Features whose parent is not the specified identifier are also ignored.
840    *
841    * @param sfs
842    * @param targetSequence
843    * @param mapping
844    * @param parentId
845    * @return
846    */
 
847  0 toggle protected boolean transferFeatures(List<SequenceFeature> sfs,
848    SequenceI targetSequence, MapList mapping, String parentId)
849    {
850  0 final boolean forwardStrand = mapping.isFromForwardStrand();
851   
852    /*
853    * sort features by start position (which corresponds to end
854    * position descending if reverse strand) so as to add them in
855    * 'forwards' order to the target sequence
856    */
857  0 SequenceFeatures.sortFeatures(sfs, forwardStrand);
858   
859  0 boolean transferred = false;
860   
861  0 for (int i = 0, n = sfs.size(); i < n; i++)
862    {
863   
864    // if ((i%1000) == 0) {
865    //// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
866    // Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);
867    // }
868   
869  0 SequenceFeature sf = sfs.get(i);
870  0 if (retainFeature(sf, parentId))
871    {
872  0 transferFeature(sf, targetSequence, mapping, forwardStrand);
873  0 transferred = true;
874    }
875    }
876   
877  0 return transferred;
878    }
879   
880    /**
881    * Answers true if the feature type is one we want to keep for the sequence.
882    * Some features are only retrieved in order to identify the sequence range,
883    * and may then be discarded as redundant information (e.g. "CDS" feature for
884    * a CDS sequence).
885    */
 
886  0 toggle @SuppressWarnings("unused")
887    protected boolean retainFeature(SequenceFeature sf, String accessionId)
888    {
889  0 return true; // override as required
890    }
891   
892    /**
893    * Answers true if the feature has a Parent which refers to the given
894    * accession id, or if the feature has no parent. Answers false if the
895    * feature's Parent is for a different accession id.
896    *
897    * @param sf
898    * @param identifier
899    * @return
900    */
 
901  10 toggle protected boolean featureMayBelong(SequenceFeature sf, String identifier)
902    {
903  10 String parent = (String) sf.getValue(PARENT);
904  10 if (parent != null
905    && !parent.equalsIgnoreCase(identifier))
906    {
907    // this genomic feature belongs to a different transcript
908  3 return false;
909    }
910  7 return true;
911    }
912   
913    /**
914    * Answers a short description of the sequence fetcher
915    */
 
916  0 toggle @Override
917    public String getDescription()
918    {
919  0 return "Ensembl " + getSourceEnsemblType().getType()
920    + " sequence with variant features";
921    }
922   
923    /**
924    * Returns a (possibly empty) list of features on the sequence which have the
925    * specified sequence ontology term (or a sub-type of it), and the given
926    * identifier as parent
927    *
928    * @param sequence
929    * @param term
930    * @param parentId
931    * @return
932    */
 
933  0 toggle protected List<SequenceFeature> findFeatures(SequenceI sequence,
934    String term, String parentId)
935    {
936  0 List<SequenceFeature> result = new ArrayList<>();
937   
938  0 List<SequenceFeature> sfs = sequence.getFeatures()
939    .getFeaturesByOntology(term);
940  0 for (SequenceFeature sf : sfs)
941    {
942  0 String parent = (String) sf.getValue(PARENT);
943  0 if (parent != null && parent.equalsIgnoreCase(parentId))
944    {
945  0 result.add(sf);
946    }
947    }
948   
949  0 return result;
950    }
951   
952    /**
953    * Answers true if the feature type is either 'NMD_transcript_variant' or
954    * 'transcript' (or one of its sub-types in the Sequence Ontology). This is
955    * because NMD_transcript_variant behaves like 'transcript' in Ensembl
956    * although strictly speaking it is not (it is a sub-type of
957    * sequence_variant).
958    * <p>
959    * (This test was needed when fetching transcript features as GFF. As we are
960    * now fetching as JSON, all features have type 'transcript' so the check for
961    * NMD_transcript_variant is redundant. Left in for any future case arising.)
962    *
963    * @param featureType
964    * @return
965    */
 
966  18 toggle public static boolean isTranscript(String featureType)
967    {
968  18 return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
969    || SequenceOntologyFactory.getInstance().isA(featureType,
970    SequenceOntologyI.TRANSCRIPT);
971    }
972    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.