dotplot: change satellite-repeat color to purple
authorMartin C. Frith
Wed Aug 21 14:32:10 2019 +0900 (3 months ago)
changeset 984fb43f850eba2
parent 983 2a722dbe737a
child 985 49caf55d4d4d
dotplot: change satellite-repeat color to purple
doc/last-dotplot.txt
scripts/last-dotplot
     1.1 --- a/doc/last-dotplot.txt	Tue Jul 16 07:51:22 2019 +0900
     1.2 +++ b/doc/last-dotplot.txt	Wed Aug 21 14:32:10 2019 +0900
     1.3 @@ -137,8 +137,8 @@
     1.4    --rmsk1=FILE
     1.5        Read repeat annotations for the 1st genome, in RepeatMasker .out
     1.6        or rmsk.txt format.  The color is pale purple for "low
     1.7 -      complexity" and "simple repeats", else pale red for "+" strand
     1.8 -      and pale blue for "-" strand.
     1.9 +      complexity", "simple repeats", and "satellites", else pale red
    1.10 +      for "+" strand and pale blue for "-" strand.
    1.11    --rmsk2=FILE
    1.12        Read repeat annotations for the 2nd genome.
    1.13  
     2.1 --- a/scripts/last-dotplot	Tue Jul 16 07:51:22 2019 +0900
     2.2 +++ b/scripts/last-dotplot	Wed Aug 21 14:32:10 2019 +0900
     2.3 @@ -647,10 +647,10 @@
     2.4              beg = int(fields[5]) - 1
     2.5              end = int(fields[6])
     2.6              strand = fields[8]
     2.7 -            repeatClass = fields[10]
     2.8 +            repeatClass = fields[10].split("/")[0]
     2.9          else:
    2.10              continue
    2.11 -        if repeatClass in ("Low_complexity", "Simple_repeat"):
    2.12 +        if repeatClass in ("Low_complexity", "Simple_repeat", "Satellite"):
    2.13              yield 200, "#fbf", seqName, beg, end
    2.14          elif (strand == "+") != rangeDict[seqName][0][2]:
    2.15              yield 100, "#ffe8e8", seqName, beg, end