rbbt-util 5.21.45 → 5.21.46

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: c5548662b8fb8f838dd581ef6fcca2c4ca2ecba7
+  metadata.gz: 1842f04355fb68456343e2efd33e3f91a392b087
+  data.tar.gz: f900fd25199c8ea1e115288ae19419a076a7b295
 SHA512:
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-  data.tar.gz: 0427bf495cddf0e82bc2c096d4df52aba8d380a9a76941966cc8800d2de2c08cc5e35ae8653338d3b113bd9ec3405c30301b2be4f32e950b7f303c41a1fdfa03
+  metadata.gz: c5acb1a420921a7929890ca011e7e40dc8bea24dde6f8d722bc97306050e70f1220c6688cd00a7c2b5ecc1ce351a8fed55458e8e62d280be9bc0de7fa49a3601
+  data.tar.gz: 606c4d21d9c52b3f466cc8f0c6dfef007fd755dffe051d99dba04dc296e8479e99b1a241cf03adaede913b78bee3732109ecc81cbb04edfcf5a0de72eebf2104

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -427,7 +427,7 @@ module TSV
         store.add *value
       when IO
         return false if value.nil?
-        value.strip!
+        value.chomp!
         store.puts value
       else
         store << value

data/lib/rbbt/tsv/serializers.rb

@@ -1,5 +1,6 @@
 module TSV
 
+
   class CleanSerializer
     def self.dump(o); o end
     def self.load(o); o end
@@ -15,14 +16,26 @@ module TSV
     def self.load(str); str.unpack("d").first; end
   end
 
-  class IntegerArraySerializer
+  class StrictIntegerArraySerializer
     def self.dump(a); a.pack("l*"); end
-    def self.load(str); str.unpack("l*"); end
+    def self.load(str); a = str.unpack("l*"); end
   end
 
-  class FloatArraySerializer
+  class StrictFloatArraySerializer
     def self.dump(a); a.pack("d*"); end
-    def self.load(str); str.unpack("d*"); end
+    def self.load(str); a = str.unpack("d*"); end
+  end
+
+  class IntegerArraySerializer
+    NIL_INT = -999
+    def self.dump(a); a.collect{|v| v || NIL_INT}.pack("l*"); end
+    def self.load(str); a = str.unpack("l*"); a.collect{|v| v == NIL_INT ? nil : v}; end
+  end
+
+  class FloatArraySerializer
+    NIL_FLOAT = -999.999
+    def self.dump(a); a.collect{|v| v || NIL_FLOAT}.pack("d*"); end
+    def self.load(str); a = str.unpack("d*"); a.collect{|v| v == NIL_FLOAT ? nil : v}; end
   end
 
   class StringSerializer
@@ -78,6 +91,8 @@ module TSV
     :float => FloatSerializer, 
     :integer_array => IntegerArraySerializer,
     :float_array => FloatArraySerializer,
+    :strict_integer_array => StrictIntegerArraySerializer,
+    :strict_float_array => StrictFloatArraySerializer,
     :marshal => Marshal,
     :single => StringSerializer,
     :string => StringSerializer,

data/share/Rlib/util.R

@@ -513,3 +513,27 @@ rbbt.ranks <- function(x){
 rbbt.default_code <- function(organism){
     return(organism + "/feb2014")
 }
+
+# Adapted from
+# http://stackoverflow.com/questions/27418461/calculate-the-modes-in-a-multimodal-distribution-in-r
+# by http://stackoverflow.com/users/6388753/ferroao
+rbbt.get.modes <- function(x,bw = NULL,spar = NULL) {  
+    if (is.null(bw)) bw = bw.nrd0(x);
+    if (is.null(spar)) spar = 0.1;
+
+    den <- density(x, kernel=c("gaussian"),bw=bw)
+    den.s <- smooth.spline(den$x, den$y, all.knots=TRUE, spar=spar)
+    s.1 <- predict(den.s, den.s$x, deriv=1)
+    s.0 <- predict(den.s, den.s$x, deriv=0)
+    den.sign <- sign(s.1$y)
+    a<-c(1,1+which(diff(den.sign)!=0))
+    b<-rle(den.sign)$values
+    df<-data.frame(a,b)
+    df = df[which(df$b %in% -1),]
+    modes<-s.1$x[df$a]
+    density<-s.0$y[df$a]
+    df2<-data.frame(modes,density)
+    df2<-df2[with(df2, order(-density)), ] # ordered by density
+    df2
+}
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.45
+  version: 5.21.46
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-10-18 00:00:00.000000000 Z
+date: 2016-10-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake