Make cleaning

jupyterhub_volumes/web/obidoc/docs/programming/lua/extrem_quality.lua

@@ -0,0 +1,59 @@
+--
+-- Script for obiscript extracting the qualities of
+-- the first `size` and last `size` base pairs of 
+-- all the reads longer than 2 x `size`
+--
+-- The result is a csv file on the stdout
+--
+-- obiscript -S ../qualities.lua FAZ61712_c61e82f1_69e58200_0_nolambda.fastq > xxxx
+
+-- Import the io module
+local io = require("io")
+
+-- Set the output stream to the stdout of the Go program
+io.output(io.stdout)
+
+size = 60
+
+function begin()
+    obicontext.item("locker", Mutex:new())
+    header = "id"
+    for i = 1, size do
+        header = header .. ", L" .. i 
+    end
+
+
+    for i = size, 1, -1 do
+        header = header .. ", R" .. i
+    end
+
+    obicontext.item("locker"):lock()
+    print(header)
+    obicontext.item("locker"):unlock()
+
+end
+
+function worker(sequence)
+    l = sequence:len()
+
+    if l > size * 2 then
+    qualities = sequence:qualities()
+    rep = sequence:id()
+
+    for i = 1, size do
+        rep = rep .. ", " .. qualities[i]
+    end
+
+    for i = size, 1, -1 do
+        rep = rep .. ", " .. qualities[l - i + 1]
+    end
+
+    obicontext.item("locker"):lock()
+    print(rep)
+    obicontext.item("locker"):unlock()
+
+    end
+
+    return BioSequenceSlice.new()
+
+end