import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.IncompleteCodonException;
import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)
{
List<SequenceI> unmappedProtein = new ArrayList<SequenceI>();
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = buildCodonColumnsMap(
+ protein, dna, unmappedProtein);
+ return alignProteinAs(protein, alignedCodons, unmappedProtein);
+ }
+
+ /**
+ * Builds a map whose key is an aligned codon position (3 alignment column
+ * numbers base 0), and whose value is a map from protein sequence to each
+ * protein's peptide residue for that codon. The map generates an ordering of
+ * the codons, and allows us to read off the peptides at each position in
+ * order to assemble 'aligned' protein sequences.
+ *
+ * @param protein
+ * the protein alignment
+ * @param dna
+ * the coding dna alignment
+ * @param unmappedProtein
+ * any unmapped proteins are added to this list
+ * @return
+ */
+ protected static Map<AlignedCodon, Map<SequenceI, AlignedCodon>> buildCodonColumnsMap(
+ AlignmentI protein, AlignmentI dna,
+ List<SequenceI> unmappedProtein)
+ {
+ /*
+ * maintain a list of any proteins with no mappings - these will be
+ * rendered 'as is' in the protein alignment as we can't align them
+ */
unmappedProtein.addAll(protein.getSequences());
List<AlignedCodonFrame> mappings = protein.getCodonFrames();
* {dnaSequence, {proteinSequence, codonProduct}} at that position. The
* comparator keeps the codon positions ordered.
*/
- Map<AlignedCodon, Map<SequenceI, String>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, String>>(
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, AlignedCodon>>(
new CodonComparator());
+
for (SequenceI dnaSeq : dna.getSequences())
{
for (AlignedCodonFrame mapping : mappings)
{
- Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
SequenceI prot = mapping.findAlignedSequence(
dnaSeq.getDatasetSequence(), protein);
if (prot != null)
{
+ Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
addCodonPositions(dnaSeq, prot, protein.getGapCharacter(),
seqMap, alignedCodons);
unmappedProtein.remove(prot);
}
}
}
- return alignProteinAs(protein, alignedCodons, unmappedProtein);
+
+ /*
+ * Finally add any unmapped peptide start residues (e.g. for incomplete
+ * codons) as if at the codon position before the second residue
+ */
+ int mappedSequenceCount = protein.getHeight() - unmappedProtein.size();
+ addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount);
+
+ return alignedCodons;
+ }
+
+ /**
+ * Scans for any protein mapped from position 2 (meaning unmapped start
+ * position e.g. an incomplete codon), and synthesizes a 'codon' for it at the
+ * preceding position in the alignment
+ *
+ * @param alignedCodons
+ * the codon-to-peptide map
+ * @param mappedSequenceCount
+ * the number of distinct sequences in the map
+ */
+ protected static void addUnmappedPeptideStarts(
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
+ int mappedSequenceCount)
+ {
+ // TODO there must be an easier way! root problem is that our mapping data
+ // model does not include phase so can't map part of a codon to a peptide
+ List<SequenceI> sequencesChecked = new ArrayList<SequenceI>();
+ AlignedCodon lastCodon = null;
+ Map<SequenceI, AlignedCodon> toAdd = new HashMap<SequenceI, AlignedCodon>();
+
+ for (Entry<AlignedCodon, Map<SequenceI, AlignedCodon>> entry : alignedCodons
+ .entrySet())
+ {
+ for (Entry<SequenceI, AlignedCodon> sequenceCodon : entry.getValue()
+ .entrySet())
+ {
+ SequenceI seq = sequenceCodon.getKey();
+ if (sequencesChecked.contains(seq))
+ {
+ continue;
+ }
+ sequencesChecked.add(seq);
+ AlignedCodon codon = sequenceCodon.getValue();
+ if (codon.peptideCol > 1)
+ {
+ System.err
+ .println("Problem mapping protein with >1 unmapped start positions: "
+ + seq.getName());
+ }
+ else if (codon.peptideCol == 1)
+ {
+ /*
+ * first position (peptideCol == 0) was unmapped - add it
+ */
+ if (lastCodon != null)
+ {
+ AlignedCodon firstPeptide = new AlignedCodon(lastCodon.pos1,
+ lastCodon.pos2, lastCodon.pos3, String.valueOf(seq
+ .getCharAt(0)), 0);
+ toAdd.put(seq, firstPeptide);
+ }
+ else
+ {
+ /*
+ * unmapped residue at start of alignment (no prior column) -
+ * 'insert' at nominal codon [0, 0, 0]
+ */
+ AlignedCodon firstPeptide = new AlignedCodon(0, 0, 0,
+ String.valueOf(seq.getCharAt(0)), 0);
+ toAdd.put(seq, firstPeptide);
+ }
+ }
+ if (sequencesChecked.size() == mappedSequenceCount)
+ {
+ // no need to check past first mapped position in all sequences
+ break;
+ }
+ }
+ lastCodon = entry.getKey();
+ }
+
+ /*
+ * add any new codons safely after iterating over the map
+ */
+ for (Entry<SequenceI, AlignedCodon> startCodon : toAdd.entrySet())
+ {
+ addCodonToMap(alignedCodons, startCodon.getValue(),
+ startCodon.getKey());
+ }
}
/**
* @return
*/
protected static int alignProteinAs(AlignmentI protein,
- Map<AlignedCodon, Map<SequenceI, String>> alignedCodons,
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
List<SequenceI> unmappedProtein)
{
/*
int column = 0;
for (AlignedCodon codon : alignedCodons.keySet())
{
- final Map<SequenceI, String> columnResidues = alignedCodons
+ final Map<SequenceI, AlignedCodon> columnResidues = alignedCodons
.get(codon);
- for (Entry<SequenceI, String> entry : columnResidues.entrySet())
+ for (Entry<SequenceI, AlignedCodon> entry : columnResidues.entrySet())
{
// place translated codon at its column position in sequence
- entry.getKey().getSequence()[column] = entry.getValue().charAt(0);
+ entry.getKey().getSequence()[column] = entry.getValue().product
+ .charAt(0);
}
column++;
}
*/
static void addCodonPositions(SequenceI dna, SequenceI protein,
char gapChar, Mapping seqMap,
- Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons)
{
Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
+
+ /*
+ * add codon positions, and their peptide translations, to the alignment
+ * map, while remembering the first codon mapped
+ */
while (codons.hasNext())
{
- AlignedCodon codon = codons.next();
- Map<SequenceI, String> seqProduct = alignedCodons.get(codon);
- if (seqProduct == null)
+ try
+ {
+ AlignedCodon codon = codons.next();
+ addCodonToMap(alignedCodons, codon, protein);
+ } catch (IncompleteCodonException e)
{
- seqProduct = new HashMap<SequenceI, String>();
- alignedCodons.put(codon, seqProduct);
+ // possible incomplete trailing codon - ignore
}
- seqProduct.put(protein, codon.product);
}
}
/**
+ * Helper method to add a codon-to-peptide entry to the aligned codons map
+ *
+ * @param alignedCodons
+ * @param codon
+ * @param protein
+ */
+ protected static void addCodonToMap(
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
+ AlignedCodon codon, SequenceI protein)
+ {
+ Map<SequenceI, AlignedCodon> seqProduct = alignedCodons.get(codon);
+ if (seqProduct == null)
+ {
+ seqProduct = new HashMap<SequenceI, AlignedCodon>();
+ alignedCodons.put(codon, seqProduct);
+ }
+ seqProduct.put(protein, codon);
+ }
+
+ /**
* Returns true if a cDNA/Protein mapping either exists, or could be made,
* between at least one pair of sequences in the two alignments. Currently,
* the logic is:
return false;
}
String name = seq2.getName();
- final DBRefEntry[] xrefs = seq1.getDBRef();
+ final DBRefEntry[] xrefs = seq1.getDBRefs();
if (xrefs != null)
{
for (DBRefEntry xref : xrefs)
}
/**
- * Constructs an alignment consisting of the mapped cds regions in the given
- * nucleotide sequences, and updates mappings to match.
+ * Constructs an alignment consisting of the mapped (CDS) regions in the given
+ * nucleotide sequences, and updates mappings to match. The new sequences are
+ * aligned as per the original sequences (with gapped columns omitted).
*
* @param dna
* aligned dna sequences
* @param mappings
* from dna to protein; these are replaced with new mappings
+ * @param gapChar
* @return an alignment whose sequences are the cds-only parts of the dna
- * sequences (or null if no cds are found)
+ * sequences (or null if no mappings are found)
*/
public static AlignmentI makeCdsAlignment(SequenceI[] dna,
- List<AlignedCodonFrame> mappings)
+ List<AlignedCodonFrame> mappings, char gapChar)
{
+ List<int[]> cdsColumns = findCdsColumns(dna);
+
+ /*
+ * create CDS sequences and new mappings
+ * (from cdna to cds, and cds to peptide)
+ */
List<AlignedCodonFrame> newMappings = new ArrayList<AlignedCodonFrame>();
List<SequenceI> cdsSequences = new ArrayList<SequenceI>();
for (AlignedCodonFrame acf : seqMappings)
{
AlignedCodonFrame newMapping = new AlignedCodonFrame();
- final List<SequenceI> mappedCds = makeCdsSequences(ds, acf,
- newMapping);
+ final List<SequenceI> mappedCds = makeCdsSequences(dnaSeq, acf,
+ cdsColumns, newMapping, gapChar);
if (!mappedCds.isEmpty())
{
cdsSequences.addAll(mappedCds);
}
AlignmentI al = new Alignment(
cdsSequences.toArray(new SequenceI[cdsSequences.size()]));
+ al.setGapCharacter(gapChar);
al.setDataset(null);
/*
}
/**
+ * Returns a consolidated list of column ranges where at least one sequence
+ * has a CDS feature. This assumes CDS features are on genomic sequence i.e.
+ * are for contiguous CDS ranges (no gaps).
+ *
+ * @param seqs
+ * @return
+ */
+ public static List<int[]> findCdsColumns(SequenceI[] seqs)
+ {
+ // TODO use refactored code from AlignViewController
+ // markColumnsContainingFeatures, not reinvent the wheel!
+
+ List<int[]> result = new ArrayList<int[]>();
+ for (SequenceI seq : seqs)
+ {
+ result.addAll(findCdsColumns(seq));
+ }
+
+ /*
+ * sort and compact the list into ascending, non-overlapping ranges
+ */
+ Collections.sort(result, new Comparator<int[]>()
+ {
+ @Override
+ public int compare(int[] o1, int[] o2)
+ {
+ return Integer.compare(o1[0], o2[0]);
+ }
+ });
+ result = MapList.coalesceRanges(result);
+
+ return result;
+ }
+
+ public static List<int[]> findCdsColumns(SequenceI seq)
+ {
+ List<int[]> result = new ArrayList<int[]>();
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ if (sfs != null)
+ {
+ for (SequenceFeature sf : sfs)
+ {
+ if (so.isA(sf.getType(), SequenceOntologyI.CDS))
+ {
+ int colStart = seq.findIndex(sf.getBegin());
+ int colEnd = seq.findIndex(sf.getEnd());
+ result.add(new int[] { colStart, colEnd });
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Answers true if all sequences have a gap at (or do not extend to) the
+ * specified column position (base 1)
+ *
+ * @param seqs
+ * @param col
+ * @return
+ */
+ public static boolean isGappedColumn(List<SequenceI> seqs, int col)
+ {
+ if (seqs != null)
+ {
+ for (SequenceI seq : seqs)
+ {
+ if (!Comparison.isGap(seq.getCharAt(col - 1)))
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Returns the column ranges (base 1) of each aligned sequence that are
+ * involved in any mapping. This is a helper method for aligning protein
+ * products of aligned transcripts.
+ *
+ * @param mappedSequences
+ * (possibly gapped) dna sequences
+ * @param mappings
+ * @return
+ */
+ protected static List<List<int[]>> getMappedColumns(
+ List<SequenceI> mappedSequences, List<AlignedCodonFrame> mappings)
+ {
+ List<List<int[]>> result = new ArrayList<List<int[]>>();
+ for (SequenceI seq : mappedSequences)
+ {
+ List<int[]> columns = new ArrayList<int[]>();
+ List<AlignedCodonFrame> seqMappings = MappingUtils
+ .findMappingsForSequence(seq, mappings);
+ for (AlignedCodonFrame mapping : seqMappings)
+ {
+ List<Mapping> maps = mapping.getMappingsForSequence(seq);
+ for (Mapping map : maps)
+ {
+ /*
+ * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
+ * Find and add the overall aligned column range for each
+ */
+ for (int[] cdsRange : map.getMap().getFromRanges())
+ {
+ int startPos = cdsRange[0];
+ int endPos = cdsRange[1];
+ int startCol = seq.findIndex(startPos);
+ int endCol = seq.findIndex(endPos);
+ columns.add(new int[] { startCol, endCol });
+ }
+ }
+ }
+ result.add(columns);
+ }
+ return result;
+ }
+
+ /**
* Helper method to make cds-only sequences and populate their mappings to
* protein products
* <p>
* (example EMBL KF591215).
*
* @param dnaSeq
- * a dna dataset sequence
+ * a dna aligned sequence
* @param mapping
* containing one or more mappings of the sequence to protein
+ * @param ungappedCdsColumns
* @param newMappings
* the new mapping to populate, from the cds-only sequences to their
* mapped protein sequences
* @return
*/
protected static List<SequenceI> makeCdsSequences(SequenceI dnaSeq,
- AlignedCodonFrame mapping, AlignedCodonFrame newMappings)
+ AlignedCodonFrame mapping, List<int[]> ungappedCdsColumns,
+ AlignedCodonFrame newMappings, char gapChar)
{
List<SequenceI> cdsSequences = new ArrayList<SequenceI>();
List<Mapping> seqMappings = mapping.getMappingsForSequence(dnaSeq);
for (Mapping seqMapping : seqMappings)
{
- SequenceI cds = makeCdsSequence(dnaSeq, seqMapping, newMappings);
+ SequenceI cds = makeCdsSequence(dnaSeq, seqMapping,
+ ungappedCdsColumns, gapChar);
cdsSequences.add(cds);
/*
* add new mappings, from dna to cds, and from cds to peptide
*/
- MapList dnaToCds = addCdsMappings(dnaSeq, cds, seqMapping,
- newMappings);
+ MapList dnaToCds = addCdsMappings(dnaSeq.getDatasetSequence(), cds,
+ seqMapping, newMappings);
/*
* transfer any features on dna that overlap the CDS
*/
- transferFeatures(dnaSeq, cds, dnaToCds, "CDS" /* SequenceOntology.CDS */);
+ transferFeatures(dnaSeq, cds, dnaToCds, null, SequenceOntologyI.CDS);
}
return cdsSequences;
}
/**
- * Transfers any co-located features on 'fromSeq' to 'toSeq', adjusting the
+ * Transfers co-located features on 'fromSeq' to 'toSeq', adjusting the
* feature start/end ranges, optionally omitting specified feature types.
+ * Returns the number of features copied.
*
* @param fromSeq
* @param toSeq
+ * @param select
+ * if not null, only features of this type are copied (including
+ * subtypes in the Sequence Ontology)
* @param mapping
* the mapping from 'fromSeq' to 'toSeq'
* @param omitting
*/
- protected static void transferFeatures(SequenceI fromSeq,
- SequenceI toSeq, MapList mapping, String... omitting)
+ public static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,
+ MapList mapping, String select, String... omitting)
{
+ SequenceI copyTo = toSeq;
+ while (copyTo.getDatasetSequence() != null)
+ {
+ copyTo = copyTo.getDatasetSequence();
+ }
+
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ int count = 0;
SequenceFeature[] sfs = fromSeq.getSequenceFeatures();
if (sfs != null)
{
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
+ if (select != null && !so.isA(type, select))
+ {
+ continue;
+ }
boolean omit = false;
for (String toOmit : omitting)
{
* locate the mapped range - null if either start or end is
* not mapped (no partial overlaps are calculated)
*/
- int[] mappedTo = mapping.locateInTo(sf.getBegin(), sf.getEnd());
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ int[] mappedTo = mapping.locateInTo(start, end);
+ /*
+ * if whole exon range doesn't map, try interpreting it
+ * as 5' or 3' exon overlapping the CDS range
+ */
+ if (mappedTo == null)
+ {
+ mappedTo = mapping.locateInTo(end, end);
+ if (mappedTo != null)
+ {
+ /*
+ * end of exon is in CDS range - 5' overlap
+ * to a range from the start of the peptide
+ */
+ mappedTo[0] = 1;
+ }
+ }
+ if (mappedTo == null)
+ {
+ mappedTo = mapping.locateInTo(start, start);
+ if (mappedTo != null)
+ {
+ /*
+ * start of exon is in CDS range - 3' overlap
+ * to a range up to the end of the peptide
+ */
+ mappedTo[1] = toSeq.getLength();
+ }
+ }
if (mappedTo != null)
{
SequenceFeature copy = new SequenceFeature(sf);
copy.setBegin(Math.min(mappedTo[0], mappedTo[1]));
copy.setEnd(Math.max(mappedTo[0], mappedTo[1]));
- toSeq.addSequenceFeature(copy);
+ copyTo.addSequenceFeature(copy);
+ count++;
}
}
}
+ return count;
}
/**
* @return
*/
protected static MapList addCdsMappings(SequenceI dnaSeq,
- SequenceI cdsSeq,
- Mapping dnaMapping, AlignedCodonFrame newMappings)
+ SequenceI cdsSeq, Mapping dnaMapping,
+ AlignedCodonFrame newMappings)
{
cdsSeq.createDatasetSequence();
* the peptide ranges taken unchanged from the dna mapping
*/
List<int[]> cdsRanges = new ArrayList<int[]>();
- cdsRanges.add(new int[] { 1, cdsSeq.getLength() });
+ SequenceI cdsDataset = cdsSeq.getDatasetSequence();
+ cdsRanges.add(new int[] { 1, cdsDataset.getLength() });
MapList cdsToPeptide = new MapList(cdsRanges, dnaMapping.getMap()
.getToRanges(), 3, 1);
- newMappings.addMap(cdsSeq.getDatasetSequence(), dnaMapping.getTo(),
- cdsToPeptide);
+ newMappings.addMap(cdsDataset, dnaMapping.getTo(), cdsToPeptide);
/*
* dna 'from' ranges map 1:1 to the contiguous extracted CDS
*/
- MapList dnaToCds = new MapList(
- dnaMapping.getMap().getFromRanges(), cdsRanges, 1, 1);
- newMappings.addMap(dnaSeq, cdsSeq.getDatasetSequence(), dnaToCds);
+ MapList dnaToCds = new MapList(dnaMapping.getMap().getFromRanges(),
+ cdsRanges, 1, 1);
+ newMappings.addMap(dnaSeq, cdsDataset, dnaToCds);
return dnaToCds;
}
/**
* Makes and returns a CDS-only sequence, where the CDS regions are identified
- * as the 'from' ranges of the mapping on the dna. Any sequence features on
- * the dna which overlap the CDS regions are copied to the new sequence.
+ * as the 'from' ranges of the mapping on the dna.
*
* @param dnaSeq
* nucleotide sequence
* @param seqMapping
* mappings from CDS regions of nucleotide
- * @param exonMappings
- * CDS-to-peptide mapping (to add to)
+ * @param ungappedCdsColumns
* @return
*/
protected static SequenceI makeCdsSequence(SequenceI dnaSeq,
- Mapping seqMapping, AlignedCodonFrame exonMappings)
+ Mapping seqMapping, List<int[]> ungappedCdsColumns, char gapChar)
{
- StringBuilder newSequence = new StringBuilder(dnaSeq.getLength());
- final char[] dna = dnaSeq.getSequence();
- int offset = dnaSeq.getStart() - 1;
+ int cdsWidth = MappingUtils.getLength(ungappedCdsColumns);
/*
- * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
+ * populate CDS columns with the aligned
+ * column character if that column is mapped (which may be a gap
+ * if an intron interrupts a codon), else with a gap
*/
- final List<int[]> dnaCdsRanges = seqMapping.getMap().getFromRanges();
- for (int[] range : dnaCdsRanges)
+ List<int[]> fromRanges = seqMapping.getMap().getFromRanges();
+ char[] cdsChars = new char[cdsWidth];
+ int pos = 0;
+ for (int[] columns : ungappedCdsColumns)
{
- // TODO handle reverse mapping as well (range[1] < range[0])
- for (int pos = range[0]; pos <= range[1]; pos++)
+ for (int i = columns[0]; i <= columns[1]; i++)
{
- newSequence.append(dna[pos - offset - 1]);
+ char dnaChar = dnaSeq.getCharAt(i - 1);
+ if (Comparison.isGap(dnaChar))
+ {
+ cdsChars[pos] = gapChar;
+ }
+ else
+ {
+ int seqPos = dnaSeq.findPosition(i - 1);
+ if (MappingUtils.contains(fromRanges, seqPos))
+ {
+ cdsChars[pos] = dnaChar;
+ }
+ else
+ {
+ cdsChars[pos] = gapChar;
+ }
+ }
+ pos++;
}
}
+ SequenceI cdsSequence = new Sequence(dnaSeq.getName(),
+ String.valueOf(cdsChars));
- SequenceI cds = new Sequence(dnaSeq.getName(),
- newSequence.toString());
+ transferDbRefs(seqMapping.getTo(), cdsSequence);
- transferDbRefs(seqMapping.getTo(), cds);
- return cds;
+ return cdsSequence;
}
/**
protected static void transferDbRefs(SequenceI from, SequenceI to)
{
String cdsAccId = FeatureProperties.getCodingFeature(DBRefSource.EMBL);
- DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(from.getDBRef(),
+ DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(from.getDBRefs(),
DBRefSource.CODINGDBS);
if (cdsRefs != null)
{
git://source.jalview.org / jalview.git / blobdiff