import java.io.IOException;
import java.text.ParseException;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
int codonStart = 1; // from CDS /codon_start
- String proteinName; // from CDS /product; TODO: use for protein description
+ String proteinName; // from CDS /product; used for protein description
String proteinId; // from CDS /protein_id
- Map<String, String> cdsProps = new Hashtable<>(); // CDS other qualifiers
+ Map<String, String> cdsProps = new Hashtable<>(); // CDS other qualifiers
}
private static final String WHITESPACE = "\\s+";
private String version; // from ID (second token)
+ private String description; // from (first) DE line
+
private int length = 128; // from ID (7th token), with usable default
private List<DBRefEntry> dbrefs; // from DR and also CDS /db_xref qualifiers
private String sequenceString; // from SQ lines
private List<CdsData> cds;
-
+
/**
* Constructor
*
{
line = parseID(line);
}
+ else if (line.startsWith("DE"))
+ {
+ line = parseDE(line);
+ }
else if (line.startsWith("DR"))
{
line = parseDR(line);
}
/**
+ * Reads sequence description from the first DE line found. Any trailing
+ * period is discarded. If there are multiple DE lines, only the first (short
+ * description) is read, the rest are ignored.
+ *
+ * @param line
+ * @return
+ * @throws IOException
+ */
+ String parseDE(String line) throws IOException
+ {
+ String desc = line.substring(2).trim();
+ if (desc.endsWith("."))
+ {
+ desc = desc.substring(0, desc.length() - 1);
+ }
+ this.description = desc;
+
+ /*
+ * pass over any additional DE lines
+ */
+ while ((line = nextLine()) != null)
+ {
+ if (!line.startsWith("DE"))
+ {
+ break;
+ }
+ }
+
+ return line;
+ }
+
+ /**
* Processes one DR line and saves as a DBRefEntry cross-reference. Returns
* the line following the line processed.
*
if (!secondaryId.isEmpty())
{
// todo: is this right? secondary id is not a version number
- // version = secondaryId;
+ // version = secondaryId;
}
}
this.dbrefs.add(new DBRefEntry(db, version, acc));
data.cdsLocation = tokens[2];
line = nextLine();
- while (line != null)
+ while (line != null)
{
if (!line.startsWith("FT ")) // 4 spaces
{
}
this.cds.add(data);
-
+
return line;
}
*
* @param value
* the first line of the translation (likely quoted)
- * @param data
+ * @param data
* @return
* @throws IOException
*/
}
data.translation = sb.toString();
-
+
return line;
}
/**
+ * Constructs and saves the sequence from parsed components
+ */
+ void assembleSequence()
+ {
+ String name = this.accession;
+ if (this.sourceDb != null)
+ {
+ name = this.sourceDb + "|" + name;
+ }
+ SequenceI seq = new Sequence(name, this.sequenceString);
+ seq.setDescription(this.description);
+
+ /*
+ * add a DBRef to itself
+ */
+ DBRefEntry selfRef = new DBRefEntry(sourceDb, version, accession);
+ int[] startEnd = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, startEnd, startEnd, 1, 1));
+ seq.addDBRef(selfRef);
+
+ for (DBRefEntry dbref : this.dbrefs)
+ {
+ seq.addDBRef(dbref);
+ }
+
+ processAllCDS(seq);
+
+ seq.deriveSequence();
+
+ addSequence(seq);
+ }
+
+ /**
+ * Process the CDS features, including generation of cross-references and
+ * mappings to the protein products (translation)
+ *
+ * @param seq
+ */
+ protected void processAllCDS(SequenceI seq)
+ {
+ /*
+ * record protein products found to avoid duplication i.e. >1 CDS with
+ * the same /protein_id [though not sure I can find an example of this]
+ */
+ Map<String, SequenceI> proteins = new HashMap<>();
+ for (CdsData data : cds)
+ {
+ processOneCDS(seq, data, proteins);
+ }
+ }
+
+ /**
* Processes the parsed CDS feature data to
* <ul>
* <li>add a CDS feature to the sequence for each CDS start-end range</li>
*
* @param SequenceI
* dna
+ * @param proteins
+ * map of protein products so far derived from CDS data
*/
- void processCDS(SequenceI dna, CdsData data)
+ void processOneCDS(SequenceI dna, CdsData data,
+ Map<String, SequenceI> proteins)
{
/*
* parse location into a list of [start, end, start, end] positions
sf.setValue(FeatureProperties.EXONPRODUCT, data.proteinName);
dna.addSequenceFeature(sf);
- }
- }
-
- /**
- * Constructs a sequence for the protein product (if there is one), and dbrefs
- * with mappings from dna to protein and the reverse
- */
- void processTranslation()
- {
- // TODO Auto-generated method stub
+ linkProteinProduct(dna, data, proteins);
+ }
}
/**
- * Constructs and saves the sequence from parsed components
+ * Constructs a sequence for the protein product for the CDS data (if there is
+ * one), and dbrefs with mappings from CDS to protein and the reverse
+ *
+ * @param dna
+ * @param data
+ * @param proteins
*/
- void assembleSequence()
+ void linkProteinProduct(SequenceI dna, CdsData data, Map<String, SequenceI> proteins)
{
- String name = this.accession;
- if (this.sourceDb != null)
+ /*
+ * check we have some data to work with
+ */
+ if (data.proteinId == null || data.translation == null)
{
- name = this.sourceDb + "|" + name;
+ return;
}
- SequenceI seq = new Sequence(name, this.sequenceString);
- for (DBRefEntry dbref : this.dbrefs)
+
+ /*
+ * Construct the protein sequence (if not already seen)
+ */
+ SequenceI protein = proteins.get(data.proteinId);
+ if (protein == null)
{
- seq.addDBRef(dbref);
+ protein = new Sequence(data.proteinId, data.translation, 1,
+ data.translation.length());
+ protein.setDescription(data.proteinName != null ? data.proteinName
+ : "Protein Product from " + sourceDb);
+ proteins.put(data.proteinId, protein);
}
-
- for (CdsData data : cds)
- {
- processCDS(seq, data);
- };
-
- processTranslation();
-
- seq.deriveSequence();
-
- addSequence(seq);
- }
-
- /**
- * Output (print) is not implemented for EMBL flat file format
- */
- @Override
- public String print(SequenceI[] seqs, boolean jvsuffix)
- {
- return null;
}
/**
return new int[] {};
}
}
+
+ /**
+ * Output (print) is not implemented for EMBL flat file format
+ */
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ return null;
+ }
}
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
-import static org.testng.Assert.assertNull;
import java.io.File;
import java.io.IOException;
import org.testng.annotations.Test;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
SequenceI seq = seqs.get(0);
assertEquals(seq.getName(), "EmblTest|J03321");
assertEquals(seq.getLength(), 7502);
+ assertEquals(seq.getDescription(), "Chlamydia trachomatis plasmid pCHL1, complete sequence");
/*
* should be 9 CDS features (one is a 'join' of two exons)
assertTrue(featureTypes.contains("CDS"));
/*
- * inspect some features (sort them for convenience of test assertions)
+ * inspect some features (sorted just for convenience of test assertions)
*/
List<SequenceFeature> features = seq.getFeatures()
.getAllFeatures("CDS");
assertEquals(sf.getPhase(), "0");
assertEquals(sf.getStrand(), 1);
assertEquals(sf.getValue("note"), "pGP7-D");
- // second exon of circular DNA!
+ // this is the second exon of circular CDS!
assertEquals(sf.getValue("exon number"), 2);
assertEquals(sf.getValue("product"), "hypothetical protein");
assertEquals(sf.getValue("transl_table"), "11");
assertEquals(sf.getValue("product"), "hypothetical protein");
/*
- * CDS at 7022-7502 is the first exon of the circular DNA CDS
+ * CDS at 7022-7502 is the first exon of the circular CDS
*/
sf = features.get(8);
assertEquals(sf.getBegin(), 7022);
assertEquals(sf.getValue("product"), "hypothetical protein");
/*
- * there are 4 'direct' (DR) dbrefs, and numerous CDS /db_xref entries,
- * some of them (e.g. INTERPRO) duplicates; sample a few here
+ * Jalview adds a dbref to 'self', and there are 4 'direct' (DR) dbrefs,
+ * and numerous CDS /db_xref entries (some e.g. INTERPRO are duplicates)
+ * sample a few here
* Note DBRefEntry constructor capitalises source
*/
List<DBRefEntry> dbrefs = seq.getDBRefs();
- assertEquals(dbrefs.size(), 31);
+ assertEquals(dbrefs.size(), 32);
+ // xref to 'self':
+ DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
+ int[] range = new int[] {1, seq.getLength()};
+ selfRef.setMap(new Mapping(null, range, range, 1, 1));
+ assertTrue(dbrefs.contains(selfRef));
+
// 1st DR line; note trailing period is removed
assertTrue(dbrefs.contains(new DBRefEntry("MD5", "0",
"d4c4942a634e3df4995fd5ac75c26a61")));
// the 4th DR line:
assertTrue(
- dbrefs.contains(new DBRefEntry("EuropePMC", "0", "PMC87941")));
+ dbrefs.contains(new DBRefEntry("EUROPEPMC", "0", "PMC87941")));
// from the first CDS feature; note canonicalisation to "UNIPROT"
assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19")));
assertTrue(dbrefs.contains(new DBRefEntry("UNIPROT", "0", "P0CE19")));
git://source.jalview.org / jalview.git / commitdiff