--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+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;
+import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
+/**
+ * A class that provides selective parsing of the EMBL flatfile format.
+ * <p>
+ * The initial implementation is limited to extracting fields used by Jalview
+ * after fetching an EMBL or EMBLCDS entry:
+ *
+ * <pre>
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * </pre>
+ *
+ * For a complete parser, it may be best to adopt that provided in
+ * https://github.com/enasequence/sequencetools/tree/master/src/main/java/uk/ac/ebi/embl/flatfile
+ * (but note this has a dependency on the Apache Commons library)
+ *
+ * @author gmcarstairs
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
+ */
+public class EmblFlatFile extends AlignFile // FileParse
+{
+ private static final String QUOTE = "\"";
+
+ /**
+ * A data bean class to hold values parsed from one CDS Feature (FT)
+ */
+ class CdsData
+ {
+ String translation; // from CDS feature /translation
+
+ String cdsLocation; // CDS /location raw value
+
+ int codonStart = 1; // from CDS /codon_start
+
+ String proteinName; // from CDS /product; used for protein description
+
+ String proteinId; // from CDS /protein_id
+
+ List<DBRefEntry> xrefs = new ArrayList<>(); // from CDS /db_xref qualifiers
+
+ Map<String, String> cdsProps = new Hashtable<>(); // CDS other qualifiers
+ }
+
+ private static final String WHITESPACE = "\\s+";
+
+ private String sourceDb;
+
+ /*
+ * values parsed from the EMBL flatfile record
+ */
+ private String accession; // from ID (first token)
+
+ 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
+
+ private String sequenceString; // from SQ lines
+
+ /*
+ * parsed CDS data fields, keyed by protein_id
+ */
+ private Map<String, CdsData> cds;
+
+ /**
+ * Constructor
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public EmblFlatFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(false, fp); // don't parse immediately
+ this.sourceDb = sourceId;
+ dbrefs = new ArrayList<>();
+
+ /*
+ * using TreeMap gives CDS sequences in alphabetical, so readable, order
+ */
+ cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+ }
+
+ /**
+ * Parses the flatfile, and if successful, saves as an annotated sequence
+ * which may be retrieved by calling {@code getSequence()}
+ *
+ * @throws IOException
+ */
+ public void parse() throws IOException
+ {
+ String line = nextLine();
+ while (line != null)
+ {
+ if (line.startsWith("ID"))
+ {
+ line = parseID(line);
+ }
+ else if (line.startsWith("DE"))
+ {
+ line = parseDE(line);
+ }
+ else if (line.startsWith("DR"))
+ {
+ line = parseDR(line);
+ }
+ else if (line.startsWith("SQ"))
+ {
+ line = parseSQ();
+ }
+ else if (line.startsWith("FT"))
+ {
+ line = parseFT(line);
+ }
+ else
+ {
+ line = nextLine();
+ }
+ }
+ buildSequence();
+ }
+
+ /**
+ * Extracts and saves the primary accession and version (SV value) from an ID
+ * line, or null if not found. Returns the next line after the one processed.
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseID(String line) throws IOException
+ {
+ String[] tokens = line.substring(2).split(";");
+
+ /*
+ * first is primary accession
+ */
+ String token = tokens[0].trim();
+ if (!token.isEmpty())
+ {
+ this.accession = token;
+ }
+
+ /*
+ * second token is 'SV versionNo'
+ */
+ if (tokens.length > 1)
+ {
+ token = tokens[1].trim();
+ if (token.startsWith("SV"))
+ {
+ String[] bits = token.trim().split(WHITESPACE);
+ this.version = bits[bits.length - 1];
+ }
+ }
+
+ /*
+ * seventh token is 'length BP'
+ */
+ if (tokens.length > 6)
+ {
+ token = tokens[6].trim();
+ String[] bits = token.trim().split(WHITESPACE);
+ try
+ {
+ this.length = Integer.valueOf(bits[0]);
+ } catch (NumberFormatException e)
+ {
+ Cache.log.error("bad length read in flatfile, line: " + line);
+ }
+ }
+
+ return nextLine();
+ }
+
+ /**
+ * 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.
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseDR(String line) throws IOException
+ {
+ String[] tokens = line.substring(2).split(";");
+ if (tokens.length > 1)
+ {
+ /*
+ * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+ */
+ String db = tokens[0].trim();
+ db = DBRefUtils.getCanonicalName(db);
+ String acc = tokens[1].trim();
+ if (acc.endsWith("."))
+ {
+ acc = acc.substring(0, acc.length() - 1);
+ }
+ String version = "0";
+ if (tokens.length > 2)
+ {
+ String secondaryId = tokens[2].trim();
+ if (!secondaryId.isEmpty())
+ {
+ // todo: is this right? secondary id is not a version number
+ // version = secondaryId;
+ }
+ }
+ this.dbrefs.add(new DBRefEntry(db, version, acc));
+ }
+
+ return nextLine();
+ }
+
+ /**
+ * Reads and saves the sequence, read from the lines following the SQ line.
+ * Whitespace and position counters are discarded. Returns the next line
+ * following the sequence data (the next line that doesn't start with
+ * whitespace).
+ *
+ * @throws IOException
+ */
+ String parseSQ() throws IOException
+ {
+ StringBuilder sb = new StringBuilder(this.length);
+ String line = nextLine();
+ while (line != null && line.startsWith(" "))
+ {
+ line = line.trim();
+ String[] blocks = line.split(WHITESPACE);
+
+ /*
+ * omit the last block (position counter) on each line
+ */
+ for (int i = 0; i < blocks.length - 1; i++)
+ {
+ sb.append(blocks[i]);
+ }
+ line = nextLine();
+ }
+ this.sequenceString = sb.toString();
+
+ return line;
+ }
+
+ /**
+ * Processes an FT line. If it declares a feature type of interest (currently,
+ * only CDS is processed), processes all of the associated lines (feature
+ * qualifiers), and returns the next line after that, otherwise simply returns
+ * the next line.
+ *
+ * @param line
+ * @return
+ * @throws IOException
+ */
+ String parseFT(String line) throws IOException
+ {
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length < 3 || !"CDS".equals(tokens[1]))
+ {
+ return nextLine();
+ }
+
+ CdsData data = new CdsData();
+ data.cdsLocation = tokens[2];
+
+ line = nextLine();
+ while (line != null)
+ {
+ if (!line.startsWith("FT ")) // 4 spaces
+ {
+ // e.g. start of next feature "FT source..."
+ break;
+ }
+
+ /*
+ * extract qualifier, e.g. FT /protein_id="CAA37824.1"
+ */
+ int slashPos = line.indexOf('/');
+ if (slashPos == -1)
+ {
+ Cache.log.error("Unexpected EMBL line ignored: " + line);
+ continue;
+ }
+ int eqPos = line.indexOf('=', slashPos + 1);
+ if (eqPos == -1)
+ {
+ // can happen, e.g. /ribosomal_slippage
+// Cache.log.error("Unexpected EMBL line ignored: " + line);
+ line = nextLine();
+ continue;
+ }
+ String qualifier = line.substring(slashPos + 1, eqPos);
+ String value = line.substring(eqPos + 1);
+ if (value.startsWith(QUOTE) && value.endsWith(QUOTE))
+ {
+ value = value.substring(1, value.length() - 1);
+ }
+
+ if ("protein_id".equals(qualifier))
+ {
+ data.proteinId = value;
+ line = nextLine();
+ }
+ else if ("codon_start".equals(qualifier))
+ {
+ try
+ {
+ data.codonStart = Integer.parseInt(value.trim());
+ } catch (NumberFormatException e)
+ {
+ Cache.log.error("Invalid codon_start in XML for " + this.accession
+ + ": " + e.getMessage());
+ }
+ line = nextLine();
+ }
+ else if ("db_xref".equals(qualifier))
+ {
+ String[] parts = value.split(":");
+ if (parts.length == 2)
+ {
+ String db = parts[0].trim();
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim());
+ data.xrefs.add(dbref);
+ }
+ line = nextLine();
+ }
+ else if ("product".equals(qualifier))
+ {
+ // sometimes name is returned e.g. for V00488
+ data.proteinName = value;
+ line = nextLine();
+ }
+ else if ("translation".equals(qualifier))
+ {
+ line = parseTranslation(value, data);
+ }
+ else if (!"".equals(value))
+ {
+ // throw anything else into the additional properties hash
+ data.cdsProps.put(qualifier, value);
+ line = nextLine();
+ }
+ }
+
+ if (data.proteinId != null)
+ {
+ this.cds.put(data.proteinId, data);
+ }
+ else
+ {
+ Cache.log.error("Ignoring CDS feature with no protein_id for "
+ + sourceDb + ":" + accession);
+ }
+
+ return line;
+ }
+
+ /**
+ * Reads and returns the CDS translation from one or more lines of the file,
+ * and returns the next line after that
+ *
+ * @param value
+ * the first line of the translation (likely quoted)
+ * @param data
+ * @return
+ * @throws IOException
+ */
+ String parseTranslation(String value, CdsData data) throws IOException
+ {
+ StringBuilder sb = new StringBuilder(this.length / 3 + 1);
+ sb.append(value.replace(QUOTE, ""));
+
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ if (!line.startsWith("FT "))
+ {
+ break; // reached next feature or other input line
+ }
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length < 2)
+ {
+ Cache.log.error("Ignoring bad EMBL line: " + line);
+ break;
+ }
+ if (tokens[1].startsWith("/"))
+ {
+ break; // next feature qualifier
+ }
+ sb.append(tokens[1].replace(QUOTE, ""));
+ }
+
+ data.translation = sb.toString();
+
+ return line;
+ }
+
+ /**
+ * Constructs and saves the sequence from parsed components
+ */
+ void buildSequence()
+ {
+ 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);
+ }
+
+ processCDSFeatures(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 processCDSFeatures(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.values())
+ {
+ processCDSFeature(seq, data, proteins);
+ }
+ }
+
+ /**
+ * Processes data for one parsed CDS feature to
+ * <ul>
+ * <li>create a protein product sequence for the translation</li>
+ * <li>create a cross-reference to protein with mapping from dna</li>
+ * <li>add a CDS feature to the sequence for each CDS start-end range</li>
+ * <li>add any CDS dbrefs to the sequence and to the protein product</li>
+ * </ul>
+ *
+ * @param SequenceI
+ * dna
+ * @param proteins
+ * map of protein products so far derived from CDS data
+ */
+ void processCDSFeature(SequenceI dna, CdsData data,
+ Map<String, SequenceI> proteins)
+ {
+ /*
+ * parse location into a list of [start, end, start, end] positions
+ */
+ int[] exons = getCdsRanges(this.accession, data.cdsLocation);
+
+ MapList maplist = buildMappingToProtein(dna, exons, data);
+
+ int exonNumber = 0;
+
+ for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
+ {
+ int exonStart = exons[xint];
+ int exonEnd = exons[xint + 1];
+ int begin = Math.min(exonStart, exonEnd);
+ int end = Math.max(exonStart, exonEnd);
+ exonNumber++;
+ String desc = String.format("Exon %d for protein EMBLCDS:%s",
+ exonNumber, data.proteinId);
+
+ SequenceFeature sf = new SequenceFeature("CDS", desc, begin, end,
+ this.sourceDb);
+ for (Entry<String, String> val : data.cdsProps.entrySet())
+ {
+ sf.setValue(val.getKey(), val.getValue());
+ }
+
+ sf.setEnaLocation(data.cdsLocation);
+ boolean forwardStrand = exonStart <= exonEnd;
+ sf.setStrand(forwardStrand ? "+" : "-");
+ sf.setPhase(String.valueOf(data.codonStart - 1));
+ sf.setValue(FeatureProperties.EXONPOS, exonNumber);
+ sf.setValue(FeatureProperties.EXONPRODUCT, data.proteinName);
+
+ dna.addSequenceFeature(sf);
+ }
+
+ boolean hasUniprotDbref = false;
+ for (DBRefEntry xref : data.xrefs)
+ {
+ dna.addDBRef(xref);
+ if (xref.getSource().equals(DBRefSource.UNIPROT))
+ {
+ /*
+ * construct (or find) the sequence for (data.protein_id, data.translation)
+ */
+ SequenceI protein = buildProteinProduct(dna, xref, data, proteins);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ xref.setMap(map);
+
+ /*
+ * add DBRefs with mappings from dna to protein and the inverse
+ */
+ DBRefEntry db1 = new DBRefEntry(sourceDb, version, accession);
+ db1.setMap(new Mapping(dna, maplist.getInverse()));
+ protein.addDBRef(db1);
+
+ hasUniprotDbref = true;
+ }
+ }
+
+ /*
+ * if we have a product (translation) but no explicit Uniprot dbref
+ * (example: EMBL M19487 protein_id AAB02592.1)
+ * then construct mappings to an assumed EMBLCDSPROTEIN accession
+ */
+ if (!hasUniprotDbref)
+ {
+ SequenceI protein = proteins.get(data.proteinId);
+ if (protein == null)
+ {
+ protein = new Sequence(data.proteinId, data.translation);
+ protein.setDescription(data.proteinName);
+ proteins.put(data.proteinId, protein);
+ }
+ // assuming CDSPROTEIN sequence version = dna version (?!)
+ DBRefEntry db1 = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+ this.version, data.proteinId);
+ protein.addDBRef(db1);
+
+ DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, this.version, data.proteinId);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ dnaToEmblProteinRef.setMap(map);
+ dna.addDBRef(dnaToEmblProteinRef);
+ }
+
+ /*
+ * comment brought forward from EmblXmlSource, lines 447-451:
+ * TODO: if retrieved from EMBLCDS, add a DBRef back to the parent EMBL
+ * sequence with the exon map; if given a dataset reference, search
+ * dataset for parent EMBL sequence if it exists and set its map;
+ * make a new feature annotating the coding contig
+ */
+ }
+
+ /**
+ * Computes a mapping from CDS positions in DNA sequence to protein product
+ * positions, with allowance for stop codon or incomplete start codon
+ *
+ * @param dna
+ * @param exons
+ * @param data
+ * @return
+ */
+ MapList buildMappingToProtein(final SequenceI dna, final int[] exons,
+ final CdsData data)
+ {
+ MapList dnaToProteinMapping = null;
+ int peptideLength = data.translation.length();
+
+ int[] proteinRange = new int[] { 1, peptideLength };
+ if (exons != null && exons.length > 0)
+ {
+ /*
+ * We were able to parse 'location'; do a final
+ * product length truncation check
+ */
+ int[] cdsRanges = adjustForProteinLength(peptideLength, exons);
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ else
+ {
+ /*
+ * workaround until we handle all 'location' formats fully
+ * e.g. X53828.1:60..1058 or <123..>289
+ */
+ Cache.log.error(String.format(
+ "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+ + " - Making up the CDNA region of (%s:%s)... may be incorrect",
+ data.cdsLocation, sourceDb, this.accession));
+
+ int completeCodonsLength = 1 - data.codonStart + dna.getLength();
+ int mappedDnaEnd = dna.getEnd();
+ if (peptideLength * 3 == completeCodonsLength)
+ {
+ // this might occur for CDS sequences where no features are marked
+ Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd();
+ }
+ else if ((peptideLength + 1) * 3 == completeCodonsLength)
+ {
+ Cache.log.warn("Assuming stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd() - 3;
+ }
+
+ if (mappedDnaEnd != -1)
+ {
+ int[] cdsRanges = new int[] {
+ dna.getStart() + (data.codonStart - 1), mappedDnaEnd };
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ }
+
+ return dnaToProteinMapping;
+ }
+
+ /**
+ * 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 xref
+ * @param data
+ * @param proteins
+ * @return
+ */
+ SequenceI buildProteinProduct(SequenceI dna, DBRefEntry xref,
+ CdsData data, Map<String, SequenceI> proteins)
+ {
+ /*
+ * check we have some data to work with
+ */
+ if (data.proteinId == null || data.translation == null)
+ {
+ return null;
+ }
+
+ /*
+ * Construct the protein sequence (if not already seen)
+ */
+ String proteinSeqName = xref.getSource() + "|" + xref.getAccessionId();
+ SequenceI protein = proteins.get(proteinSeqName);
+ if (protein == null)
+ {
+ protein = new Sequence(proteinSeqName, data.translation, 1,
+ data.translation.length());
+ protein.setDescription(data.proteinName != null ? data.proteinName
+ : "Protein Product from " + sourceDb);
+ proteins.put(proteinSeqName, protein);
+ }
+
+ return protein;
+ }
+
+ /**
+ * Returns the CDS location as a single array of [start, end, start, end...]
+ * positions. If on the reverse strand, these will be in descending order.
+ *
+ * @param accession
+ * @param location
+ * @return
+ */
+ protected int[] getCdsRanges(String accession, String location)
+ {
+ if (location == null)
+ {
+ return new int[] {};
+ }
+
+ try
+ {
+ List<int[]> ranges = DnaUtils.parseLocation(location);
+ return MappingUtils.listToArray(ranges);
+ } catch (ParseException e)
+ {
+ Cache.log.warn(
+ String.format("Not parsing inexact CDS location %s in ENA %s",
+ location, accession));
+ return new int[] {};
+ }
+ }
+
+ /**
+ * Output (print) is not implemented for EMBL flat file format
+ */
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ return null;
+ }
+
+ /**
+ * Truncates (if necessary) the exon intervals to match 3 times the length of
+ * the protein; also accepts 3 bases longer (for stop codon not included in
+ * protein)
+ *
+ * @param proteinLength
+ * @param exon
+ * an array of [start, end, start, end...] intervals
+ * @return the same array (if unchanged) or a truncated copy
+ */
+ static int[] adjustForProteinLength(int proteinLength, int[] exon)
+ {
+ if (proteinLength <= 0 || exon == null)
+ {
+ return exon;
+ }
+ int expectedCdsLength = proteinLength * 3;
+ int exonLength = MappingUtils.getLength(Arrays.asList(exon));
+
+ /*
+ * if exon length matches protein, or is shorter, or longer by the
+ * length of a stop codon (3 bases), then leave it unchanged
+ */
+ if (expectedCdsLength >= exonLength
+ || expectedCdsLength == exonLength - 3)
+ {
+ return exon;
+ }
+
+ int origxon[];
+ int sxpos = -1;
+ int endxon = 0;
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length; x += 2)
+ {
+ cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
+ if (expectedCdsLength <= cdspos)
+ {
+ // advanced beyond last codon.
+ sxpos = x;
+ if (expectedCdsLength != cdspos)
+ {
+ // System.err
+ // .println("Truncating final exon interval on region by "
+ // + (cdspos - cdslength));
+ }
+
+ /*
+ * shrink the final exon - reduce end position if forward
+ * strand, increase it if reverse
+ */
+ if (exon[x + 1] >= exon[x])
+ {
+ endxon = exon[x + 1] - cdspos + expectedCdsLength;
+ }
+ else
+ {
+ endxon = exon[x + 1] + cdspos - expectedCdsLength;
+ }
+ break;
+ }
+ }
+
+ if (sxpos != -1)
+ {
+ // and trim the exon interval set if necessary
+ int[] nxon = new int[sxpos + 2];
+ System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+ nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+ // set
+ exon = nxon;
+ }
+ return exon;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff