diff -r 1ecdbf2ddb78 -r 6e8ff424ce2b scripts/last-dotplot
--- a/scripts/last-dotplot	Thu May 18 14:06:41 2017 +0900
+++ b/scripts/last-dotplot	Thu May 18 14:23:58 2017 +0900
@@ -306,6 +306,55 @@
                     color = "#f4f4ff"
         yield layer, color, seqName, beg, end
 
+def commaSeparatedInts(text):
+    return map(int, text.rstrip(",").split(","))
+
+def readGenePred(opts, fileName, seqLimits):
+    if not fileName: return
+    for line in myOpen(fileName):
+        fields = line.split()
+        if not fields: continue
+        if fields[2] not in "+-": fields = fields[1:]
+        seqName = fields[1]
+        if seqName not in seqLimits: continue
+        #strand = fields[2]
+        cdsBeg = int(fields[5])
+        cdsEnd = int(fields[6])
+        exonBegs = commaSeparatedInts(fields[8])
+        exonEnds = commaSeparatedInts(fields[9])
+        for beg, end in zip(exonBegs, exonEnds):
+            yield 300, opts.exon_color, seqName, beg, end
+            b = max(beg, cdsBeg)
+            e = min(end, cdsEnd)
+            if b < e: yield 400, opts.cds_color, seqName, b, e
+
+def readRmsk(fileName, seqLimits):
+    if not fileName: return
+    for line in myOpen(fileName):
+        fields = line.split()
+        if len(fields) == 17:  # rmsk.txt
+            seqName = fields[5]
+            if seqName not in seqLimits: continue  # do this ASAP for speed
+            beg = int(fields[6])
+            end = int(fields[7])
+            strand = fields[9]
+            repeatClass = fields[11]
+        elif len(fields) == 15:  # .out
+            seqName = fields[4]
+            if seqName not in seqLimits: continue
+            beg = int(fields[5]) - 1
+            end = int(fields[6])
+            strand = fields[8]
+            repeatClass = fields[10]
+        else:
+            continue
+        if repeatClass in ("Low_complexity", "Simple_repeat"):
+            yield 200, "#ffe4ff", seqName, beg, end
+        elif strand == "+":
+            yield 100, "#fff4f4", seqName, beg, end
+        else:
+            yield 100, "#f4f4ff", seqName, beg, end
+
 def isExtraFirstGapField(fields):
     return fields[4].isdigit()
 
@@ -448,10 +497,14 @@
     origins2 = expandedSeqDict(origins2)
 
     beds1 = itertools.chain(readBed(opts.bed1, seqLimits1),
+                            readRmsk(opts.rmsk1, seqLimits1),
+                            readGenePred(opts, opts.genePred1, seqLimits1),
                             readGaps(opts, opts.gap1, seqLimits1))
     b1 = bedBoxes(beds1, seqLimits1, origins1, margin2, height, True, bpPerPix)
 
     beds2 = itertools.chain(readBed(opts.bed2, seqLimits2),
+                            readRmsk(opts.rmsk2, seqLimits2),
+                            readGenePred(opts, opts.genePred2, seqLimits2),
                             readGaps(opts, opts.gap2, seqLimits2))
     b2 = bedBoxes(beds2, seqLimits2, origins2, margin1, width, False, bpPerPix)
 
@@ -522,10 +575,6 @@
     op.add_option("--border-color", metavar="COLOR", default="#dcdcdc",
                   help="color for pixels between sequences (default=%default)")
     # xxx --margin-color?
-    op.add_option("--bed1", metavar="FILE",
-                  help="read genome1 annotations from bed file")
-    op.add_option("--bed2", metavar="FILE",
-                  help="read genome2 annotations from bed file")
 
     og = optparse.OptionGroup(op, "Text options")
     og.add_option("-f", "--fontfile", metavar="FILE",
@@ -538,6 +587,28 @@
                   help="show sequence lengths for the 2nd (vertical) genome")
     op.add_option_group(og)
 
+    og = optparse.OptionGroup(op, "Annotation options")
+    og.add_option("--bed1", metavar="FILE",
+                  help="read genome1 annotations from BED file")
+    og.add_option("--bed2", metavar="FILE",
+                  help="read genome2 annotations from BED file")
+    og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
+                  "RepeatMasker .out or rmsk.txt file")
+    og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
+                  "RepeatMasker .out or rmsk.txt file")
+    op.add_option_group(og)
+
+    og = optparse.OptionGroup(op, "Gene options")
+    og.add_option("--genePred1", metavar="FILE",
+                  help="read genome1 genes from genePred file")
+    og.add_option("--genePred2", metavar="FILE",
+                  help="read genome2 genes from genePred file")
+    og.add_option("--exon-color", metavar="COLOR", default="#dfd",
+                  help="color for exons (default=%default)")
+    og.add_option("--cds-color", metavar="COLOR", default="#bdb",
+                  help="color for protein-coding regions (default=%default)")
+    op.add_option_group(og)
+
     og = optparse.OptionGroup(op, "Unsequenced gap options")
     og.add_option("--gap1", metavar="FILE",
                   help="read genome1 unsequenced gaps from agp or gap file")