Make cleaning

jupyterhub_volumes/web/obidoc/docs/programming/expression/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Expression language on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/expression/</link>
+    <description>Recent content in Expression language on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/expression/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

jupyterhub_volumes/web/obidoc/docs/programming/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Programming OBITools on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/</link>
+    <description>Recent content in Programming OBITools on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

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

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+function begin()
+    obicontext.item("compteur",0)
+end
+
+function worker(sequence)
+    samples = sequence:attribute("merged_sample")
+    samples["tutu"]=4
+    sequence:attribute("merged_sample",samples)
+    sequence:attribute("toto",44444)
+    nb = obicontext.inc("compteur")
+    sequence:id("seq_" .. nb)
+    return sequence
+end
+
+function finish()
+    print("compteur = " .. obicontext.item("compteur"))
+end

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

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+--
+-- 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

jupyterhub_volumes/web/obidoc/docs/programming/lua/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Lua: for scripting OBITools on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/lua/</link>
+    <description>Recent content in Lua: for scripting OBITools on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/lua/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

jupyterhub_volumes/web/obidoc/docs/programming/lua/obitools_classes/biosequence/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>BioSequence on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/biosequence/</link>
+    <description>Recent content in BioSequence on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/biosequence/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

jupyterhub_volumes/web/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>BioSequenceSlice on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/</link>
+    <description>Recent content in BioSequenceSlice on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

jupyterhub_volumes/web/obidoc/docs/programming/lua/obitools_classes/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Obitools Classes on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/</link>
+    <description>Recent content in Obitools Classes on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

jupyterhub_volumes/web/obidoc/docs/programming/lua/obitools_classes/mutex/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Mutex on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/mutex/</link>
+    <description>Recent content in Mutex on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/mutex/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

jupyterhub_volumes/web/obidoc/docs/programming/lua/obitools_classes/taxon/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Taxon on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/taxon/</link>
+    <description>Recent content in Taxon on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/taxon/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>

jupyterhub_volumes/web/obidoc/docs/programming/lua/obitools_classes/taxonomy/index.xml

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+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Taxonomy on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/taxonomy/</link>
+    <description>Recent content in Taxonomy on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/programming/lua/obitools_classes/taxonomy/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>