examples/groovy/ComputePeptideVariants.groovy

   1 import jalview.datamodel.SequenceFeature
   2 import jalview.gui.Desktop
   3 def af = jalview.bin.Jalview.currentAlignFrame
   4 def av = af.viewport
   5 def fr = Desktop.getAlignFrameFor(av.codingComplement).getFeatureRenderer()
   6 def counts = 0
   7 def countm = 0
   8 for (seq in av.alignment.sequences)
   9 {
  10    ds = seq.datasetSequence
  11    for (res = ds.start ; res <= ds.end; res++)
  12    {
  13      mf = fr.findComplementFeaturesAtResidue(seq, res)
  14      if (mf != null)
  15      {
  16          for (feature in mf.features)
  17          {
  18            variant = mf.findProteinVariants(feature)
  19            if (!"".equals(variant))
  20            {
  21                type = variant.contains("=") ? "synonymous_variant" : "missense_variant"
  22                if (type.equals("synonymous_variant")) counts++ else countm++;
  23                sf = new SequenceFeature(type, variant, res, res, null)
  24                seq.addSequenceFeature(sf)
  25            }
  26          }
  27      }
  28    }
  29 }
  30 af.getFeatureRenderer().featuresAdded()
  31 af.alignPanel.paintAlignment(true, true)
  32 println "Added " + countm + " missense and " + counts + " synonymous variants"