diff --git a/Makefile b/Makefile
index b674fc53..500c0d2e 100644
--- a/Makefile
+++ b/Makefile
@@ -105,7 +105,7 @@ test_para: $(OUTPUT2)
 
 clean:
 	@make bats_cmd CMD=clean
-	@git checkout docs/manual/source/conf.py pygtftk/version.py; rm -rf pygtftk.egg-info build airway_love.txt* ENCFF630HEX_Total_RNAseq_K562_count_mini.txt STDIN.e* STDIN.o* dist cmd_list.txt example_list.txt tmp_list.txt simple.chromInfo prgm_list.txt test_list.txt *.bats *.completed *mini_real* heatmap_* tx_classes* *~ \#* hh profile_* toto tott;  cd docs/manual/; make clean; cd ../..; find . -type f -name '*~' -exec rm -f '{}' \; 
+	@git checkout docs/manual/source/conf.py pygtftk/version.py; rm -rf pygtftk.egg-info build airway_love.txt* ENCFF630HEX_Total_RNAseq_K562_count_mini.txt STDIN.e* closest_1.tsv STDIN.o* dist cmd_list.txt example_list.txt tmp_list.txt simple.chromInfo prgm_list.txt test_list.txt *.bats *.completed *mini_real* heatmap_* tx_classes* *~ \#* hh profile_* toto tott;  cd docs/manual/; make clean; cd ../..; find . -type f -name '*~' -exec rm -f '{}' \; 
 
 check_cmd_has_example:
 	@for i in $$(gtftk -l); do if grep -q  "^$$i" docs/manual/source/presentation.rst; then echo "" >/dev/null; else echo $$i; fi; done
@@ -116,15 +116,10 @@ check_example_has_cmd:
 	@for i in $$(cat example_list.txt); do if $$(cat cmd_list.txt  | grep -q "^$$i")  ; then echo "" >/dev/null; else echo $$i; fi; done
 	@#rm -f cmd_list.txt example_list.txt tmp_list.txt
 
-prepare_pip:
-	@touch pypi_release_in_progress
-	@rm -rf build/ dist/ pygtftk.egg-info/
-	@python setup.py sdist
-	@python setup.py bdist_wheel
-	@rm -f pypi_release_in_progress
-
-send_to_pypi:
-	@twine upload --repository-url https://test.pypi.org/legacy/ dist/* --verbose
-
 nb_test:
 	@gtftk -p| perl -ne 'BEGIN{$$/="{"}{/\@test\s+"(\w+)_\d+"/; print $$1,"\n"}'| sort | uniq -c | sort -nr
+release:
+	@touch release_in_progress
+
+unrelease:
+	@rm -f release_in_progress
diff --git a/README.md b/README.md
index 3bae091e..2d243d89 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,10 @@
-[![Packagist](https://img.shields.io/packagist/l/doctrine/orm.svg)](https://github.com/dputhier/gtftk) [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/dputhier/gtftk/issues) [![HitCount](http://hits.dwyl.io/puthier/gtftk.svg)](http://hits.dwyl.io/puthier/gtftk) 
-![GitHub release](https://img.shields.io/github/release/qubyte/rubidium.svg)
+[![Packagist](https://img.shields.io/packagist/l/doctrine/orm.svg)](https://github.com/dputhier/pygtftk) [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/dputhier/pygtftk/issues) [![HitCount](http://hits.dwyl.com/dputhier/pygtftk.svg)](http://hits.dwyl.com/dputhier/pygtftk)
 
 
 # Python GTF toolkit (pygtftk)
 
 
-The **Python GTF toolkit (pygtftk) package** is intented to ease handling of GTF (Gene Transfer Format) files. The pygtftk package is compatible with Python 2.7 and relies on **libgtftk**, a library of functions **written in C**. 
+The **Python GTF toolkit (pygtftk) package** is intented to ease handling of GTF (Gene Transfer Format) files. The pygtftk package is compatible with Python 2.7 and Python >=3.5 and relies on **libgtftk**, a library of functions **written in C**. 
 
 The package comes with a set of **UNIX commands** that can be accessed through the **gtftk  program**. The gtftk program proposes several atomic tools to filter, convert, or extract data from GTF files. The gtftk set of Unix commands can be easily extended using a basic plugin architecture. All these aspects are covered in the help sections.
 
@@ -13,20 +12,19 @@ While the gtftk Unix program comes with hundreds of unitary and functional tests
 
 ## System requirements
 
-Depending on the **size of the GTF file**, pygtftk may require lot of memory to perform selected tasks. A computer with 16Go is recommended in order to be able to pipe several commands when working with human annotations from ensembl release (e.g. 91).
+Depending on the **size of the GTF file**, pygtftk and gtftk may require lot of memory to perform selected tasks. A computer with 16Go is recommended in order to be able to pipe several commands when working with human annotations from ensembl release (e.g. 91).
 
 At the moment, the gtftk program has been tested on:
 
 - Linux (Ubuntu 12.04 and 18.04)
 - OSX (Yosemite, El Capitan).
-- WSL/Bash on Ubuntu on Windows.
 
 
 ## Installation through conda package building
 
-Installation through **conda** should be the **prefered install solution**. Although the GTF interface of pygtftk should work properly after a pip install (see next section), the UNIX commands (gtftk program) require several external dependencies with some version constrains.
+Installation through **conda** should be the **prefered install solution**. The pygtftk package and gtftk command line tool require external dependencies with some version constrains (e.g. bedtools that, we observed, displays some back compatibility issue).
 
-At the moment, there is no built conda package available. You can however create an environment with all prerequisites using the commands below.
+A conda package will be available in the near future. In the meantime, you can however create an environment with all prerequisites using the commands below.
 If conda is not available on your system, first install miniconda from the official [web site](http://conda.pydata.org/miniconda.html).
 
     git clone git@github.com:dputhier/pygtftk.git pygtftk
@@ -34,30 +32,27 @@ If conda is not available on your system, first install miniconda from the offic
     conda env create -n pygtftk_py3k -f conda/env.yaml python=3.6
     source activate pygtftk_py3k
     make install
+    # It is important to call gtftk -h
+    # to find and dump plugin parsers
+    # before going further
+    gtftk -h 
 
-Note for developpers: You can install the develop branch using the same approach.
-
-    git clone git@github.com:dputhier/pygtftk.git pygtftk
-    cd pygtftk
-    git checkout develop
-    conda env create -n pygtftk_py3k_dev -f conda/env.yaml python=3.6
-    source activate pygtftk_py3k_dev
-    make install
-    
 ## Installation through pip 
 
 ### Prerequesites
  
-Again, this is not the prefered way for installation. Please choose conda whenever possible. The gtftk Unix command line program requires at least bedtools (command line).
+Again, this is not the prefered way for installation. Please choose conda whenever possible. The gtftk Unix command line program has been tested with bedtools 2.27.1 (be aware that we have encountered some back compatibility issues with bedtools).
 
 ### Running pip 
 
 Installation through pip can be done as follow.
 
     pip install -r requirements.txt
-
     pip install pygtftk
-    
+    # It is important to call gtftk -h
+    # to find and dump plugin parsers
+    # before going further
+    gtftk -h     
 
 ## Running functional tests
 
diff --git a/bin/__init__.py b/bin/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/changelog.md b/changelog.md
index 8d7309dc..fbd585a1 100644
--- a/changelog.md
+++ b/changelog.md
@@ -1,21 +1,34 @@
-## Changelog
+# Changelog
 
-### v0.9.2 (not-yet-release)
+## v0.9.4 (not-yet-release)
 
-#### Bug Fixes
+### Bug Fixes
 
-#### API Changes
+### API Changes
 
+### New Features
 
-#### New Features
 
-- pygtftk is now compatible with both python 2 and 3.
+## v0.9.3
+
+### Bug Fixes
+
+- User-defined colors are now applied when calling profile command (bug in 0.9.2).
+- Fixed test issues when using md5sum under Linux.
+- Lots of typo fixed (their must be lot remaining unfortunatly...).
+
+### API Changes
+
+
+### New Features
+
+- pygtftk is now compatible with both python 2.7 and >=3.5.
 - libstdcxx is no more required in env.yaml.
 - 'Makefile clean' also reset version.py and conf.py to repository version.
 - Improved parser loading.
 - 5p_3p_coord has been renamed get_5p_3p_coords.
-- Lots of typo fixed (their must be lot remaining unfortunatly...).
 - Added a pip requirement.txt file for developers.
 - Added a specific conda environment file for py2k.
-- The default conda environment targets Python3.6.
+- The default conda environment targets Python 3.6.
 - Improve garbage collector behavior upon exit.
+- Added --system-info argument to gtftk.
diff --git a/conda/env.yaml b/conda/env.yaml
index d9810825..81c1cee4 100644
--- a/conda/env.yaml
+++ b/conda/env.yaml
@@ -17,8 +17,6 @@ dependencies:
     - pandas >=0.23.3
     - scipy >=1.1.0
     - pybedtools >=0.7.8
-    - pybigwig >=0.3.10
-    - pysam >=0.9.1.4
     - pyyaml >=3.12
     - gcc >=4.8.5
     - requests >=2.13.0
@@ -30,4 +28,6 @@ dependencies:
     - plotnine >=0.4.0
     - pip:
       - future
+      - pyBigWig >=0.3.12
+      - future
 
diff --git a/conda/env_py2k.yaml b/conda/env_py2k.yaml
index 182d7927..b62ecc32 100644
--- a/conda/env_py2k.yaml
+++ b/conda/env_py2k.yaml
@@ -18,7 +18,6 @@ dependencies:
     - scipy >=1.1.0
     - pybedtools >=0.7.8
     - pybigwig >=0.3.10
-    - pysam >=0.9.1.4
     - pyyaml >=3.12
     - gcc >=4.8.5
     - requests >=2.13.0
@@ -26,8 +25,9 @@ dependencies:
     - pyparsing >=2.2.0
     - biopython >=1.69
     - zlib >=1.2.11
-    - matplotlib >=2.0.2
+    - matplotlib >=2.0.2,<3
     - plotnine >=0.4.0
     - pip:
       - future
-      - sphinxcontrib-programoutput
\ No newline at end of file
+      - pyBigWig >=0.3.12
+      - future
\ No newline at end of file
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 2ebfc3b9..a9b15544 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -21,7 +21,6 @@ requirements:
     - scipy >=1.1.0
     - pybedtools >=0.7.8
     - pybigwig >=0.3.10
-    - pysam >=0.9.1.4
     - pyyaml >=3.12
     - gcc >=4.8.5
     - requests >=2.13.0
@@ -33,6 +32,8 @@ requirements:
     - plotnine >=0.4.0
     - pip:
       - future
+      - pyBigWig >=0.3.12
+      - future
 
   run:
     - GitPython >=2.1.8
@@ -46,7 +47,6 @@ requirements:
     - scipy >=1.1.0
     - pybedtools >=0.7.8
     - pybigwig >=0.3.10
-    - pysam >=0.9.1.4
     - pyyaml >=3.12
     - gcc >=4.8.5
     - requests >=2.13.0
@@ -58,6 +58,8 @@ requirements:
     - plotnine >=0.4.0
     - pip:
       - future
+      - pyBigWig >=0.3.12
+      - future
 
 test:
   commands:
diff --git a/conda/meta_py2k.yaml b/conda/meta_py2k.yaml
index 5caed5b5..d72e24bf 100644
--- a/conda/meta_py2k.yaml
+++ b/conda/meta_py2k.yaml
@@ -20,8 +20,6 @@ requirements:
     - pandas >=0.23.3
     - scipy >=1.1.0
     - pybedtools >=0.7.8
-    - pybigwig >=0.3.10
-    - pysam >=0.9.1.4
     - pyyaml >=3.12
     - gcc >=4.8.5
     - requests >=2.13.0
@@ -29,10 +27,12 @@ requirements:
     - pyparsing >=2.2.0
     - biopython >=1.69
     - zlib >=1.2.11
-    - matplotlib >=2.0.2
+    - matplotlib >=2.0.2,<3
     - plotnine >=0.4.0
     - pip:
       - future
+      - pybigwig >=0.3.12
+      - future
 
   run:
     - GitPython >=2.1.8
@@ -45,8 +45,6 @@ requirements:
     - pandas >=0.23.3
     - scipy >=1.1.0
     - pybedtools >=0.7.8
-    - pybigwig >=0.3.10
-    - pysam >=0.9.1.4
     - pyyaml >=3.12
     - gcc >=4.8.5
     - requests >=2.13.0
@@ -54,10 +52,12 @@ requirements:
     - pyparsing >=2.2.0
     - biopython >=1.69
     - zlib >=1.2.11
-    - matplotlib >=2.0.2
+    - matplotlib >=2.0.2,<3
     - plotnine >=0.4.0
     - pip:
       - future
+      - pybigwig >=0.3.12
+      - future
 
 test:
   commands:
diff --git a/docs/manual/build/html/.buildinfo b/docs/manual/build/html/.buildinfo
index dd634509..54d8aaf3 100644
--- a/docs/manual/build/html/.buildinfo
+++ b/docs/manual/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5bba3f85f3e759061303af1056946e93
+config: 3eeb7851cd4315f822ba357e4cc51edd
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/manual/build/html/_static/documentation_options.js b/docs/manual/build/html/_static/documentation_options.js
index 5535fbf7..482f48fb 100644
--- a/docs/manual/build/html/_static/documentation_options.js
+++ b/docs/manual/build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.9.2',
+    VERSION: '0.9.3',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',
diff --git a/docs/manual/build/html/about.html b/docs/manual/build/html/about.html
index a9cb2d2d..7b0462ae 100644
--- a/docs/manual/build/html/about.html
+++ b/docs/manual/build/html/about.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>About pygtftk &#8212; gtftk 0.9.2 documentation</title>
+    <title>About pygtftk &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -35,7 +35,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="&lt;no title&gt;"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -199,7 +199,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="&lt;no title&gt;"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/api.html b/docs/manual/build/html/api.html
index 53b088b3..1127f473 100644
--- a/docs/manual/build/html/api.html
+++ b/docs/manual/build/html/api.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Help on Python package (pygtftk) &#8212; gtftk 0.9.2 documentation</title>
+    <title>Help on Python package (pygtftk) &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -35,7 +35,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="presentation.html" title="Help on gtftk Unix commands"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -3265,7 +3265,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="presentation.html" title="Help on gtftk Unix commands"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/bwig_coverage.html b/docs/manual/build/html/bwig_coverage.html
index ef41cdee..e4bf4885 100644
--- a/docs/manual/build/html/bwig_coverage.html
+++ b/docs/manual/build/html/bwig_coverage.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>The gtftk.bam.bam_coverage_matrix module &#8212; gtftk 0.9.2 documentation</title>
+    <title>The gtftk.bam.bam_coverage_matrix module &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -35,7 +35,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="api.html" title="Help on Python package (pygtftk)"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -157,7 +157,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="api.html" title="Help on Python package (pygtftk)"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/developers.html b/docs/manual/build/html/developers.html
index 8cf05e5e..23688614 100644
--- a/docs/manual/build/html/developers.html
+++ b/docs/manual/build/html/developers.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Writing your own commands &#8212; gtftk 0.9.2 documentation</title>
+    <title>Writing your own commands &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -31,7 +31,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="bwig_coverage.html" title="The gtftk.bam.bam_coverage_matrix module"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -232,7 +232,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="bwig_coverage.html" title="The gtftk.bam.bam_coverage_matrix module"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/example_01.png b/docs/manual/build/html/example_01.png
index 8381b9d1..dc5a7c25 100644
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index 131467f8..2c72253a 100644
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index 131467f8..b22f767d 100644
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index c075c049..d583f6d7 100644
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index c19172cc..15e0e117 100644
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diff --git a/docs/manual/build/html/example_13.png b/docs/manual/build/html/example_13.png
index d549e551..3e5657cc 100644
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diff --git a/docs/manual/build/html/genindex.html b/docs/manual/build/html/genindex.html
index 7993aff7..ccbb93d8 100644
--- a/docs/manual/build/html/genindex.html
+++ b/docs/manual/build/html/genindex.html
@@ -7,7 +7,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Index &#8212; gtftk 0.9.2 documentation</title>
+    <title>Index &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -485,7 +485,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/index.html b/docs/manual/build/html/index.html
index 8cf71d37..574a1aa2 100644
--- a/docs/manual/build/html/index.html
+++ b/docs/manual/build/html/index.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>&lt;no title&gt; &#8212; gtftk 0.9.2 documentation</title>
+    <title>&lt;no title&gt; &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -31,7 +31,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="about.html" title="About pygtftk"
              accesskey="N">next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -119,7 +119,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="about.html" title="About pygtftk"
              >next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/installation.html b/docs/manual/build/html/installation.html
index ed7988a0..217e9bdf 100644
--- a/docs/manual/build/html/installation.html
+++ b/docs/manual/build/html/installation.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Installing pygtftk/gtftk &#8212; gtftk 0.9.2 documentation</title>
+    <title>Installing pygtftk/gtftk &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -35,7 +35,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="about.html" title="About pygtftk"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -99,7 +99,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="about.html" title="About pygtftk"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/objects.inv b/docs/manual/build/html/objects.inv
index 308df731..3f036ccf 100644
Binary files a/docs/manual/build/html/objects.inv and b/docs/manual/build/html/objects.inv differ
diff --git a/docs/manual/build/html/presentation.html b/docs/manual/build/html/presentation.html
index 2dafd885..ae100482 100644
--- a/docs/manual/build/html/presentation.html
+++ b/docs/manual/build/html/presentation.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Help on gtftk Unix commands &#8212; gtftk 0.9.2 documentation</title>
+    <title>Help on gtftk Unix commands &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -35,7 +35,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="installation.html" title="Installing pygtftk/gtftk"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -52,7 +52,7 @@ <h2>Main parser arguments of gtftk<a class="headerlink" href="#main-parser-argum
 <h3>Getting help with -h<a class="headerlink" href="#getting-help-with-h" title="Permalink to this headline">¶</a></h3>
 <p>The -h argument can be used to get a synopsis for implemented commands.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk -h
-  Usage: gtftk [-h] [-b] [-p] [-v] [-l]  ...
+  Usage: gtftk [-h] [-b] [-p] [-s] [-v] [-l]  ...
 
   A toolbox to handle GTF files.
 
@@ -66,7 +66,7 @@ <h3>Getting help with -h<a class="headerlink" href="#getting-help-with-h" title=
   gtftk select_by_key -k feature -v transcript |   gtftk tabulate -k &quot;*&quot; -b
   
 
-  Use &#39;gtftk sub-command -h&#39; for more information.
+  Type &#39;gtftk sub-command -h&#39; for more information.
 
     
 
@@ -74,6 +74,7 @@ <h3>Getting help with -h<a class="headerlink" href="#getting-help-with-h" title=
  -h, --help                   show this help message and exit
  -b, --bash-comp              Get a script to activate bash completion. (default: False)
  -p, --plugin-tests           Display bats tests for all plugin. (default: False)
+ -s, --system-info            Display some info about the system. (default: False)
  -v, --version                show program&#39;s version number and exit
  -l, --list-plugins           Get the list of plugins. (default: False)
 
@@ -216,9 +217,9 @@ <h3>apropos<a class="headerlink" href="#apropos" title="Permalink to this headli
 <p><strong>Description:</strong> Search in all command description files those related to a user-defined keyword.</p>
 <p><strong>Example:</strong> Search all commands related to promoters.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk apropos -k promoter
- |-- 12:56-INFO-apropos : &gt;&gt; Keyword &#39;promoter&#39; was found in the following command:
-	- coverage.
+ |-- 11:06-INFO-apropos : &gt;&gt; Keyword &#39;promoter&#39; was found in the following command:
 	- divergent.
+	- coverage.
 </pre></div>
 </div>
 <p><strong>Arguments:</strong></p>
@@ -313,36 +314,36 @@ <h3>get_example<a class="headerlink" href="#get-example" title="Permalink to thi
 </div>
 <p>let’s get all files from the <em>simple</em> dataset.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk get_example -d simple -f &#39;*&#39;
- |-- 12:56-INFO-get_example : Copying: add_attr_to_pos.tab
- |-- 12:56-INFO-get_example : Copying: simple.1.bt2
- |-- 12:56-INFO-get_example : Copying: simple.2.bt2
- |-- 12:56-INFO-get_example : Copying: simple.2.bw
- |-- 12:56-INFO-get_example : Copying: simple.3.bt2
- |-- 12:56-INFO-get_example : Copying: simple.3.bw
- |-- 12:56-INFO-get_example : Copying: simple.4.bt2
- |-- 12:56-INFO-get_example : Copying: simple.bam
- |-- 12:56-INFO-get_example : Copying: simple.bam.bai
- |-- 12:56-INFO-get_example : Copying: simple.bw
- |-- 12:56-INFO-get_example : Copying: simple.chromInfo
- |-- 12:56-INFO-get_example : Copying: simple.fa
- |-- 12:56-INFO-get_example : Copying: simple.fa.fai
- |-- 12:56-INFO-get_example : Copying: simple.geneList
- |-- 12:56-INFO-get_example : Copying: simple.genes
- |-- 12:56-INFO-get_example : Copying: simple.gtf
- |-- 12:56-INFO-get_example : Copying: simple.join
- |-- 12:56-INFO-get_example : Copying: simple.join_mat
- |-- 12:56-INFO-get_example : Copying: simple.join_mat_2
- |-- 12:56-INFO-get_example : Copying: simple.join_mat_3
- |-- 12:56-INFO-get_example : Copying: simple.join_with_dup
- |-- 12:56-INFO-get_example : Copying: simple.loc_bed
- |-- 12:56-INFO-get_example : Copying: simple.map
- |-- 12:56-INFO-get_example : Copying: simple.rev.1.bt2
- |-- 12:56-INFO-get_example : Copying: simple.rev.2.bt2
- |-- 12:56-INFO-get_example : Copying: simple_col.csv
- |-- 12:56-INFO-get_example : Copying: simple_peaks.bed
- |-- 12:56-INFO-get_example : Copying: simple_peaks.bed3
- |-- 12:56-INFO-get_example : Copying: simple_peaks.bed6
- |-- 12:56-INFO-get_example : Copying: simple_reads.fq
+ |-- 11:07-INFO-get_example : Copying: add_attr_to_pos.tab
+ |-- 11:07-INFO-get_example : Copying: simple.1.bt2
+ |-- 11:07-INFO-get_example : Copying: simple.2.bt2
+ |-- 11:07-INFO-get_example : Copying: simple.2.bw
+ |-- 11:07-INFO-get_example : Copying: simple.3.bt2
+ |-- 11:07-INFO-get_example : Copying: simple.3.bw
+ |-- 11:07-INFO-get_example : Copying: simple.4.bt2
+ |-- 11:07-INFO-get_example : Copying: simple.bam
+ |-- 11:07-INFO-get_example : Copying: simple.bam.bai
+ |-- 11:07-INFO-get_example : Copying: simple.bw
+ |-- 11:07-INFO-get_example : Copying: simple.chromInfo
+ |-- 11:07-INFO-get_example : Copying: simple.fa
+ |-- 11:07-INFO-get_example : Copying: simple.fa.fai
+ |-- 11:07-INFO-get_example : Copying: simple.geneList
+ |-- 11:07-INFO-get_example : Copying: simple.genes
+ |-- 11:07-INFO-get_example : Copying: simple.gtf
+ |-- 11:07-INFO-get_example : Copying: simple.join
+ |-- 11:07-INFO-get_example : Copying: simple.join_mat
+ |-- 11:07-INFO-get_example : Copying: simple.join_mat_2
+ |-- 11:07-INFO-get_example : Copying: simple.join_mat_3
+ |-- 11:07-INFO-get_example : Copying: simple.join_with_dup
+ |-- 11:07-INFO-get_example : Copying: simple.loc_bed
+ |-- 11:07-INFO-get_example : Copying: simple.map
+ |-- 11:07-INFO-get_example : Copying: simple.rev.1.bt2
+ |-- 11:07-INFO-get_example : Copying: simple.rev.2.bt2
+ |-- 11:07-INFO-get_example : Copying: simple_col.csv
+ |-- 11:07-INFO-get_example : Copying: simple_peaks.bed
+ |-- 11:07-INFO-get_example : Copying: simple_peaks.bed3
+ |-- 11:07-INFO-get_example : Copying: simple_peaks.bed6
+ |-- 11:07-INFO-get_example : Copying: simple_reads.fq
 </pre></div>
 </div>
 <p><strong>Arguments:</strong></p>
@@ -1182,22 +1183,22 @@ <h3>merge_attr<a class="headerlink" href="#merge-attr" title="Permalink to this
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk get_example |  gtftk merge_attr -k transcript_id,gene_id -d transcript_id -s &quot;|&quot; -f &quot;*&quot; | gtftk tabulate -k feature,transcript_id -x | head -n 6
 Traceback (most recent call last):
   File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/bin/gtftk&quot;, line 4, in &lt;module&gt;
-    __import__(&#39;pkg_resources&#39;).run_script(&#39;pygtftk==0.9.1.dev0+7f5a&#39;, &#39;gtftk&#39;)
+    __import__(&#39;pkg_resources&#39;).run_script(&#39;pygtftk==0.9.3&#39;, &#39;gtftk&#39;)
   File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pkg_resources/__init__.py&quot;, line 661, in run_script
     self.require(requires)[0].run_script(script_name, ns)
   File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pkg_resources/__init__.py&quot;, line 1441, in run_script
     exec(code, namespace, namespace)
-  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.1.dev0+7f5a-py3.6-macosx-10.9-x86_64.egg/EGG-INFO/scripts/gtftk&quot;, line 83, in &lt;module&gt;
+  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.3-py3.6-macosx-10.9-x86_64.egg/EGG-INFO/scripts/gtftk&quot;, line 83, in &lt;module&gt;
     args = main()
-  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.1.dev0+7f5a-py3.6-macosx-10.9-x86_64.egg/EGG-INFO/scripts/gtftk&quot;, line 68, in main
+  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.3-py3.6-macosx-10.9-x86_64.egg/EGG-INFO/scripts/gtftk&quot;, line 68, in main
     CmdManager.run(args)
-  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.1.dev0+7f5a-py3.6-macosx-10.9-x86_64.egg/pygtftk/cmd_manager.py&quot;, line 939, in run
+  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.3-py3.6-macosx-10.9-x86_64.egg/pygtftk/cmd_manager.py&quot;, line 977, in run
     fun(**args)
-  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.1.dev0+7f5a-py3.6-macosx-10.9-x86_64.egg/pygtftk/plugins/merge_attr.py&quot;, line 92, in merge_attr
+  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.3-py3.6-macosx-10.9-x86_64.egg/pygtftk/plugins/merge_attr.py&quot;, line 92, in merge_attr
     separator).write(outputfile,
-  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.1.dev0+7f5a-py3.6-macosx-10.9-x86_64.egg/pygtftk/gtf_interface.py&quot;, line 536, in merge_attr
+  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.3-py3.6-macosx-10.9-x86_64.egg/pygtftk/gtf_interface.py&quot;, line 538, in merge_attr
     self = self.add_attr_column(tmp_file, new_key)
-  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.1.dev0+7f5a-py3.6-macosx-10.9-x86_64.egg/pygtftk/gtf_interface.py&quot;, line 3363, in add_attr_column
+  File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pygtftk-0.9.3-py3.6-macosx-10.9-x86_64.egg/pygtftk/gtf_interface.py&quot;, line 3369, in add_attr_column
     tmp = input_file.readlines()
   File &quot;/Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/tempfile.py&quot;, line 485, in func_wrapper
     return func(*args, **kwargs)
@@ -1239,7 +1240,7 @@ <h3>discretize_key<a class="headerlink" href="#discretize-key" title="Permalink
 The default is to create equally spaced interval. The intervals can also be created by computing the percentiles (-p).</p>
 <p><strong>Example:</strong> Let say we have the following matrix giving expression level of genes (rows) in samples (columns). We could join this information to the GTF and later choose to transform key <em>S1</em> into a new discretized key <em>S1_d</em>. We may apply particular labels to this factor using <em>-l</em>.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk get_example |  gtftk join_attr -j simple.join_mat -k gene_id -m | gtftk discretize_key -k S1 -d S1_d -n 2 | gtftk select_by_key -k feature -v gene
- |-- 12:58-INFO-discretize_key : Categories: [&#39;(0.231_0.616]&#39;, &#39;(0.616_0.999]&#39;]
+ |-- 11:08-INFO-discretize_key : Categories: [&#39;(0.231_0.616]&#39;, &#39;(0.616_0.999]&#39;]
 chr1	gtftk	gene	125	138	.	+	.	gene_id &quot;G0001&quot;;
 chr1	gtftk	gene	180	189	.	+	.	gene_id &quot;G0002&quot;;
 chr1	gtftk	gene	50	61	.	-	.	gene_id &quot;G0003&quot;; S1 &quot;0.2322&quot;; S2 &quot;0.4&quot;; S1_d &quot;(0.231_0.616]&quot;;
@@ -1253,7 +1254,7 @@ <h3>discretize_key<a class="headerlink" href="#discretize-key" title="Permalink
 </pre></div>
 </div>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk get_example |  gtftk join_attr -j simple.join_mat -k gene_id -m | gtftk discretize_key -k S1 -d S1_d -n 2 -l A,B  | gtftk select_by_key -k feature -v gene
- |-- 12:58-INFO-discretize_key : Categories: [&#39;A&#39;, &#39;B&#39;]
+ |-- 11:08-INFO-discretize_key : Categories: [&#39;A&#39;, &#39;B&#39;]
 chr1	gtftk	gene	125	138	.	+	.	gene_id &quot;G0001&quot;;
 chr1	gtftk	gene	180	189	.	+	.	gene_id &quot;G0002&quot;;
 chr1	gtftk	gene	50	61	.	-	.	gene_id &quot;G0003&quot;; S1 &quot;0.2322&quot;; S2 &quot;0.4&quot;; S1_d &quot;A&quot;;
@@ -1654,7 +1655,7 @@ <h3>random_list<a class="headerlink" href="#random-list" title="Permalink to thi
 <p><strong>Example:</strong> Select randomly 3 transcripts.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk get_example | gtftk random_list -n 3| gtftk count
 transcript	3
-exon	4
+exon	3
 CDS	3
 </pre></div>
 </div>
@@ -1696,12 +1697,12 @@ <h3>random_tx<a class="headerlink" href="#random-tx" title="Permalink to this he
 G0001	G0001T002
 G0002	G0002T001
 G0003	G0003T001
-G0004	G0004T002
+G0004	G0004T001
 G0005	G0005T001
-G0006	G0006T001
+G0006	G0006T002
 G0007	G0007T002
 G0008	G0008T001
-G0009	G0009T001
+G0009	G0009T002
 G0010	G0010T001
 </pre></div>
 </div>
@@ -2993,24 +2994,24 @@ <h3>coverage<a class="headerlink" href="#coverage" title="Permalink to this head
 <div><strong>Example:</strong></div></blockquote>
 <p>We will first request a lightweight example dataset.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk get_example -d mini_real -f &#39;*&#39;
- |-- 13:01-INFO-get_example : Copying: #H3K4me3_cond_1.bed#
- |-- 13:01-INFO-get_example : Copying: airway_love.txt.gz
- |-- 13:01-INFO-get_example : Copying: ENCFF112BHN_H3K4me3_K562_sub.bed
- |-- 13:01-INFO-get_example : Copying: ENCFF119BYM_H3K36me3_K562_sub.bed
- |-- 13:01-INFO-get_example : Copying: ENCFF431HAA_H3K36me3_K562_sub.bw
- |-- 13:01-INFO-get_example : Copying: ENCFF742FDS_H3K4me3_K562_sub.bw
- |-- 13:01-INFO-get_example : Copying: ENCFF947DVY_H3K79me2_K562_sub.bw
- |-- 13:01-INFO-get_example : Copying: H3K4me3_cond_1.bed
- |-- 13:01-INFO-get_example : Copying: H3K4me3_cond_2.bed
- |-- 13:01-INFO-get_example : Copying: H3K4me3_cond_3.bed
- |-- 13:01-INFO-get_example : Copying: hg38.genome
- |-- 13:01-INFO-get_example : Copying: hg38.genome.back
- |-- 13:01-INFO-get_example : Copying: mini_real.gtf.gz
- |-- 13:01-INFO-get_example : Copying: mini_real_control_1.txt
- |-- 13:01-INFO-get_example : Copying: mini_real_counts_ENCFF630HEX.txt
- |-- 13:01-INFO-get_example : Copying: mini_real_gn_list_hg38.txt
- |-- 13:01-INFO-get_example : Copying: mini_real_noov_rnd_tx.gtf.gz
- |-- 13:01-INFO-get_example : Copying: tx_classes.txt
+ |-- 11:41-INFO-get_example : Copying: #H3K4me3_cond_1.bed#
+ |-- 11:41-INFO-get_example : Copying: airway_love.txt.gz
+ |-- 11:41-INFO-get_example : Copying: ENCFF112BHN_H3K4me3_K562_sub.bed
+ |-- 11:41-INFO-get_example : Copying: ENCFF119BYM_H3K36me3_K562_sub.bed
+ |-- 11:41-INFO-get_example : Copying: ENCFF431HAA_H3K36me3_K562_sub.bw
+ |-- 11:41-INFO-get_example : Copying: ENCFF742FDS_H3K4me3_K562_sub.bw
+ |-- 11:41-INFO-get_example : Copying: ENCFF947DVY_H3K79me2_K562_sub.bw
+ |-- 11:41-INFO-get_example : Copying: H3K4me3_cond_1.bed
+ |-- 11:41-INFO-get_example : Copying: H3K4me3_cond_2.bed
+ |-- 11:41-INFO-get_example : Copying: H3K4me3_cond_3.bed
+ |-- 11:41-INFO-get_example : Copying: hg38.genome
+ |-- 11:41-INFO-get_example : Copying: hg38.genome.back
+ |-- 11:41-INFO-get_example : Copying: mini_real.gtf.gz
+ |-- 11:41-INFO-get_example : Copying: mini_real_control_1.txt
+ |-- 11:41-INFO-get_example : Copying: mini_real_counts_ENCFF630HEX.txt
+ |-- 11:41-INFO-get_example : Copying: mini_real_gn_list_hg38.txt
+ |-- 11:41-INFO-get_example : Copying: mini_real_noov_rnd_tx.gtf.gz
+ |-- 11:41-INFO-get_example : Copying: tx_classes.txt
 </pre></div>
 </div>
 <p>Although we could work on the full dataset, we will focus on transcripts whose promoter region do not overlaps with any transcript from another gene.</p>
@@ -3101,24 +3102,24 @@ <h3>mk_matrix<a class="headerlink" href="#mk-matrix" title="Permalink to this he
 Will will create tree example datasets:</p>
 <p>First we will create a coverage matrix around promoter based on a subset of randomly choose transcripts (one per gene) from the ‘mini_real’ dataset (see section on the <em>coverage</em> command to get info about the construction of the <em>mini_real_noov_rnd_tx.gtf.gz</em> dataset).</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk get_example -f &#39;*&#39; -d mini_real
- |-- 13:01-INFO-get_example : Copying: #H3K4me3_cond_1.bed#
- |-- 13:01-INFO-get_example : Copying: airway_love.txt.gz
- |-- 13:01-INFO-get_example : Copying: ENCFF112BHN_H3K4me3_K562_sub.bed
- |-- 13:01-INFO-get_example : Copying: ENCFF119BYM_H3K36me3_K562_sub.bed
- |-- 13:01-INFO-get_example : Copying: ENCFF431HAA_H3K36me3_K562_sub.bw
- |-- 13:01-INFO-get_example : Copying: ENCFF742FDS_H3K4me3_K562_sub.bw
- |-- 13:01-INFO-get_example : Copying: ENCFF947DVY_H3K79me2_K562_sub.bw
- |-- 13:01-INFO-get_example : Copying: H3K4me3_cond_1.bed
- |-- 13:01-INFO-get_example : Copying: H3K4me3_cond_2.bed
- |-- 13:01-INFO-get_example : Copying: H3K4me3_cond_3.bed
- |-- 13:01-INFO-get_example : Copying: hg38.genome
- |-- 13:01-INFO-get_example : Copying: hg38.genome.back
- |-- 13:01-INFO-get_example : Copying: mini_real.gtf.gz
- |-- 13:01-INFO-get_example : Copying: mini_real_control_1.txt
- |-- 13:01-INFO-get_example : Copying: mini_real_counts_ENCFF630HEX.txt
- |-- 13:01-INFO-get_example : Copying: mini_real_gn_list_hg38.txt
- |-- 13:01-INFO-get_example : Copying: mini_real_noov_rnd_tx.gtf.gz
- |-- 13:01-INFO-get_example : Copying: tx_classes.txt
+ |-- 11:41-INFO-get_example : Copying: #H3K4me3_cond_1.bed#
+ |-- 11:41-INFO-get_example : Copying: airway_love.txt.gz
+ |-- 11:41-INFO-get_example : Copying: ENCFF112BHN_H3K4me3_K562_sub.bed
+ |-- 11:41-INFO-get_example : Copying: ENCFF119BYM_H3K36me3_K562_sub.bed
+ |-- 11:41-INFO-get_example : Copying: ENCFF431HAA_H3K36me3_K562_sub.bw
+ |-- 11:41-INFO-get_example : Copying: ENCFF742FDS_H3K4me3_K562_sub.bw
+ |-- 11:41-INFO-get_example : Copying: ENCFF947DVY_H3K79me2_K562_sub.bw
+ |-- 11:41-INFO-get_example : Copying: H3K4me3_cond_1.bed
+ |-- 11:41-INFO-get_example : Copying: H3K4me3_cond_2.bed
+ |-- 11:41-INFO-get_example : Copying: H3K4me3_cond_3.bed
+ |-- 11:41-INFO-get_example : Copying: hg38.genome
+ |-- 11:41-INFO-get_example : Copying: hg38.genome.back
+ |-- 11:41-INFO-get_example : Copying: mini_real.gtf.gz
+ |-- 11:41-INFO-get_example : Copying: mini_real_control_1.txt
+ |-- 11:41-INFO-get_example : Copying: mini_real_counts_ENCFF630HEX.txt
+ |-- 11:41-INFO-get_example : Copying: mini_real_gn_list_hg38.txt
+ |-- 11:41-INFO-get_example : Copying: mini_real_noov_rnd_tx.gtf.gz
+ |-- 11:41-INFO-get_example : Copying: tx_classes.txt
 </pre></div>
 </div>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk mk_matrix -k 5 -i mini_real_noov_rnd_tx.gtf.gz -d 5000 -u 5000 -w 200 -c hg38.genome  -l  H3K4me3,H3K79me,H3K36me3 ENCFF742FDS_H3K4me3_K562_sub.bw ENCFF947DVY_H3K79me2_K562_sub.bw ENCFF431HAA_H3K36me3_K562_sub.bw -o mini_real_promoter
@@ -3130,38 +3131,42 @@ <h3>mk_matrix<a class="headerlink" href="#mk-matrix" title="Permalink to this he
 </div>
 <p>The following command compute coverage profil along the whole transcript</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk mk_matrix -k 5 -i mini_real_noov_rnd_tx.gtf.gz -t transcript  -d 5000 -u 5000 -w 200 -c hg38.genome  -l  H3K4me3,H3K79me,H3K36me3 ENCFF742FDS_H3K4me3_K562_sub.bw ENCFF947DVY_H3K79me2_K562_sub.bw ENCFF431HAA_H3K36me3_K562_sub.bw -o mini_real_tx
- |-- 13:02-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:02-WARNING-mk_matrix : ENST00000612829 has length : 85
- |-- 13:02-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:02-WARNING-mk_matrix : Filter them out please.
- |-- 13:02-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:02-WARNING-mk_matrix : ENST00000385018 has length : 82
- |-- 13:02-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:02-WARNING-mk_matrix : Filter them out please.
- |-- 13:02-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:02-WARNING-mk_matrix : ENST00000583764 has length : 85
- |-- 13:02-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:02-WARNING-mk_matrix : Filter them out please.
+ |-- 11:42-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:42-WARNING-mk_matrix : ENST00000612829 has length : 85
+ |-- 11:42-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:42-WARNING-mk_matrix : Filter them out please.
+ |-- 11:42-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:42-WARNING-mk_matrix : ENST00000385018 has length : 82
+ |-- 11:42-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:42-WARNING-mk_matrix : Filter them out please.
+ |-- 11:42-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:42-WARNING-mk_matrix : ENST00000583764 has length : 85
+ |-- 11:42-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:42-WARNING-mk_matrix : Filter them out please.
+ |-- 11:42-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:42-WARNING-mk_matrix : ENST00000637495 has length : 68
+ |-- 11:42-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:42-WARNING-mk_matrix : Filter them out please.
 </pre></div>
 </div>
 <p>Along the whole transcript but increasing the number of windows dedicated to upstream and downstream regions.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk mk_matrix -k 5 --bin-around-frac 0.5 -i mini_real_noov_rnd_tx.gtf.gz -t transcript  -d 5000 -u 5000 -w 200 -c hg38.genome  -l  H3K4me3,H3K79me,H3K36me3 ENCFF742FDS_H3K4me3_K562_sub.bw ENCFF947DVY_H3K79me2_K562_sub.bw ENCFF431HAA_H3K36me3_K562_sub.bw -o mini_real_tx_2
- |-- 13:03-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:03-WARNING-mk_matrix : ENST00000612829 has length : 85
- |-- 13:03-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:03-WARNING-mk_matrix : Filter them out please.
- |-- 13:03-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:03-WARNING-mk_matrix : ENST00000385018 has length : 82
- |-- 13:03-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:03-WARNING-mk_matrix : Filter them out please.
- |-- 13:03-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:03-WARNING-mk_matrix : ENST00000583764 has length : 85
- |-- 13:03-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:03-WARNING-mk_matrix : Filter them out please.
- |-- 13:03-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:03-WARNING-mk_matrix : ENST00000637495 has length : 68
- |-- 13:03-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:03-WARNING-mk_matrix : Filter them out please.
+ |-- 11:43-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:43-WARNING-mk_matrix : ENST00000612829 has length : 85
+ |-- 11:43-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:43-WARNING-mk_matrix : Filter them out please.
+ |-- 11:43-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:43-WARNING-mk_matrix : ENST00000385018 has length : 82
+ |-- 11:43-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:43-WARNING-mk_matrix : Filter them out please.
+ |-- 11:43-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:43-WARNING-mk_matrix : ENST00000583764 has length : 85
+ |-- 11:43-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:43-WARNING-mk_matrix : Filter them out please.
+ |-- 11:43-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:43-WARNING-mk_matrix : ENST00000637495 has length : 68
+ |-- 11:43-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:43-WARNING-mk_matrix : Filter them out please.
 </pre></div>
 </div>
 <p>Along a user defined set of regions (in bed6 format). Here we will used the transcript coordinates in bed format as an example.</p>
@@ -3169,22 +3174,22 @@ <h3>mk_matrix<a class="headerlink" href="#mk-matrix" title="Permalink to this he
 </pre></div>
 </div>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk mk_matrix -k 5 --bin-around-frac 0.5 -i mini_real_rnd_tx.bed -t user_regions  -d 5000 -u 5000 -w 200 -c hg38.genome  -l  H3K4me3,H3K79me,H3K36me3 ENCFF742FDS_H3K4me3_K562_sub.bw ENCFF947DVY_H3K79me2_K562_sub.bw ENCFF431HAA_H3K36me3_K562_sub.bw -o mini_real_user_def
- |-- 13:04-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:04-WARNING-mk_matrix : ENSG00000187514|ENST00000612829 has length : 85
- |-- 13:04-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:04-WARNING-mk_matrix : Filter them out please.
- |-- 13:04-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:04-WARNING-mk_matrix : ENSG00000207751|ENST00000385018 has length : 82
- |-- 13:04-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:04-WARNING-mk_matrix : Filter them out please.
- |-- 13:04-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:04-WARNING-mk_matrix : ENSG00000110717|ENST00000583764 has length : 85
- |-- 13:04-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:04-WARNING-mk_matrix : Filter them out please.
- |-- 13:04-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 13:04-WARNING-mk_matrix : ENSG00000148120|ENST00000637495 has length : 68
- |-- 13:04-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 13:04-WARNING-mk_matrix : Filter them out please.
+ |-- 11:45-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:45-WARNING-mk_matrix : ENSG00000187514|ENST00000612829 has length : 85
+ |-- 11:45-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:45-WARNING-mk_matrix : Filter them out please.
+ |-- 11:44-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:44-WARNING-mk_matrix : ENSG00000207751|ENST00000385018 has length : 82
+ |-- 11:44-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:44-WARNING-mk_matrix : Filter them out please.
+ |-- 11:45-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:45-WARNING-mk_matrix : ENSG00000110717|ENST00000583764 has length : 85
+ |-- 11:45-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:45-WARNING-mk_matrix : Filter them out please.
+ |-- 11:45-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 11:45-WARNING-mk_matrix : ENSG00000148120|ENST00000637495 has length : 68
+ |-- 11:45-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 11:45-WARNING-mk_matrix : Filter them out please.
 </pre></div>
 </div>
 <p>And finally using a set of single nucleotides coordinates that will be extend (-u/-d) and assessed for coverage. Here we will take the coordinates of TSS as example.</p>
@@ -3203,132 +3208,132 @@ <h3>profile<a class="headerlink" href="#profile" title="Permalink to this headli
 <p><strong>Basic profiles</strong></p>
 <p>A simple overlayed profile of all epigenetic marks around promoter. Here <em>—group-by</em> is, by default set to <em>bwig</em> and <em>—facet-var</em> is set to None. Thus a single plot with several lines corresponding to bwig coverage is obtained.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if example_01.png
- |-- 13:05-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:46-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_01.png"><img alt="example_01.png" src="example_01.png" style="width: 75%;" /></a>
 <p>The same diagram is obtained if a bed file pointing to TSS was provided to <em>mk_matrix</em> and used in <em>single_nuc</em> mode.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -i mini_real_single_nuc.zip -o profile_prom -pf png -if example_01a.png
- |-- 13:05-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:46-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_01a.png"><img alt="example_01a.png" src="example_01a.png" style="width: 75%;" /></a>
 <p>Changing colors and applying color order can be done using the following syntax:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -c &#39;red,blue,violet&#39; -d H3K79me,H3K4me3,H3K36me3 -o profile_prom -pf png -if example_01b.png
- |-- 13:06-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:46-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_01b.png"><img alt="example_01b.png" src="example_01b.png" style="width: 75%;" /></a>
 <p>A subset of bigwig assessed for coverage can be selected for plotting. This is achieved using the <em>–subset-bwig</em> argument:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -f bwig -g tx_classes -D -i mini_real_tx.zip  -fo  -o profile_tx -pf png -if example_01c.png  -fo -c &#39;red&#39; -V 2  -w  -tl -e -lw 0.5 -u H3K4me3
- |-- 13:06-DEBUG-profile : Using pandas version 0.23.4
- |-- 13:06-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
- |-- 13:06-DEBUG-profile : Using numpy version 1.13.3
- |-- 13:06-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
- |-- 13:06-DEBUG-profile : Using plotnine version 0.4.0
- |-- 13:06-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
- |-- 13:06-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_1xvoz2cs
- |-- 13:06-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_1xvoz2cs/mini_real_tx
- |-- 13:06-INFO-profile : Getting configuration info from input file.
- |-- 13:06-DEBUG-profile : Color order :[&#39;All transcripts&#39;]
- |-- 13:06-DEBUG-profile : Profile color :[&#39;red&#39;]
- |-- 13:06-INFO-profile : Searching coverage columns.
- |-- 13:06-INFO-profile : Melting.
- |-- 13:06-INFO-profile : Ceiling
- |-- 13:06-INFO-profile : Zero value detected. Adding a pseudocount (+1) before log transformation.
- |-- 13:06-INFO-profile : Converting to log2.
- |-- 13:06-INFO-profile : Computing column ordering.
- |-- 13:06-INFO-profile : Preparing diagram
- |-- 13:06-INFO-profile : Theming and ordering. Please be patient...
- |-- 13:06-INFO-profile : Preparing x axis
- |-- 13:06-INFO-profile : facet_col 1
- |-- 13:06-INFO-profile : Highlighting upstream regions
- |-- 13:06-INFO-profile : Page width set to 4
- |-- 13:06-INFO-profile : Page height set to 2.0
- |-- 13:06-INFO-profile : Saving diagram to file : example_01c.png
- |-- 13:06-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:46-DEBUG-profile : Using pandas version 0.23.4
+ |-- 11:46-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
+ |-- 11:46-DEBUG-profile : Using numpy version 1.13.3
+ |-- 11:46-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
+ |-- 11:46-DEBUG-profile : Using plotnine version 0.4.0
+ |-- 11:46-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
+ |-- 11:46-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_jbh1ifex
+ |-- 11:46-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_jbh1ifex/mini_real_tx
+ |-- 11:46-INFO-profile : Getting configuration info from input file.
+ |-- 11:46-DEBUG-profile : Color order :[&#39;All transcripts&#39;]
+ |-- 11:46-DEBUG-profile : Profile color :[&#39;red&#39;]
+ |-- 11:46-INFO-profile : Searching coverage columns.
+ |-- 11:46-INFO-profile : Melting.
+ |-- 11:46-INFO-profile : Ceiling
+ |-- 11:46-INFO-profile : Zero value detected. Adding a pseudocount (+1) before log transformation.
+ |-- 11:46-INFO-profile : Converting to log2.
+ |-- 11:46-INFO-profile : Computing column ordering.
+ |-- 11:46-INFO-profile : Preparing diagram
+ |-- 11:46-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:46-INFO-profile : Preparing x axis
+ |-- 11:46-INFO-profile : facet_col 1
+ |-- 11:46-INFO-profile : Highlighting upstream regions
+ |-- 11:46-INFO-profile : Page width set to 4
+ |-- 11:46-INFO-profile : Page height set to 2.0
+ |-- 11:46-INFO-profile : Saving diagram to file : example_01c.png
+ |-- 11:46-INFO-profile : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_01c.png"><img alt="example_01c.png" src="example_01c.png" style="width: 75%;" /></a>
 <p>Transcript coverage is obtained using the <em>mini_real_tx.zip</em> matrix. This provides a simple overlayed profile of all epigenetic marks along the transcript body extended in 5’ and 3’ regions:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_tx.zip -o profile_tx -pf png -if example_02.png
- |-- 13:06-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:46-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_02.png"><img alt="example_02.png" src="example_02.png" style="width: 75%;" /></a>
 <p>Almost the same but increasing the bins dedicated to upstream and dowstream regions (see <em>—bin-around-frac argument of *mk_matrix</em>).</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_tx_2.zip -o profile_tx -pf png -if example_03.png
- |-- 13:06-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:46-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_03.png"><img alt="example_03.png" src="example_03.png" style="width: 75%;" /></a>
 <p>Note that the same is obtained when using user-defined regions (<em>i.e</em> when providing a bed as input corresponding to transcript coordinates).</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_user_def.zip -o profile_udef_4  -pf png -if example_04.png
- |-- 13:06-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:47-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_04.png"><img alt="example_04.png" src="example_04.png" style="width: 75%;" /></a>
 <p>The same dataset used for plotting but adding a normalization step (<em>ranging</em>). When using <em>ranging</em> normalization, values are expressed as a percentage of the range between max and min value.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -nm ranging -i mini_real_user_def.zip -o profile_udef_5  -pf png -if example_04b.png
- |-- 13:06-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:47-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_04b.png"><img alt="example_04b.png" src="example_04b.png" style="width: 75%;" /></a>
 <p>Two examples using statistic ‘max’ and 2 differents values of ‘–upper-limit’.</p>
 <blockquote>
 <div><div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if example_04_max_a.png  -V 2 -lw 1 -at 5 -s max -ul 1
- |-- 13:06-DEBUG-profile : Using pandas version 0.23.4
- |-- 13:06-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
- |-- 13:06-DEBUG-profile : Using numpy version 1.13.3
- |-- 13:06-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
- |-- 13:06-DEBUG-profile : Using plotnine version 0.4.0
- |-- 13:06-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
- |-- 13:06-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_qdroqb06
- |-- 13:06-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_qdroqb06/mini_real_promoter
- |-- 13:06-INFO-profile : Getting configuration info from input file.
- |-- 13:06-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
- |-- 13:06-DEBUG-profile : Color order :[&#39;H3K79me&#39;, &#39;H3K36me3&#39;, &#39;H3K4me3&#39;]
- |-- 13:06-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
- |-- 13:06-INFO-profile : Searching coverage columns.
- |-- 13:06-INFO-profile : Melting.
- |-- 13:06-INFO-profile : Computing column ordering.
- |-- 13:06-INFO-profile : Preparing diagram
- |-- 13:06-INFO-profile : Theming and ordering. Please be patient...
- |-- 13:06-INFO-profile : Preparing x axis
- |-- 13:06-INFO-profile : facet_col 1
- |-- 13:06-INFO-profile : Page width set to 3
- |-- 13:06-INFO-profile : Page height set to 2
- |-- 13:06-INFO-profile : Saving diagram to file : example_04_max_a.png
- |-- 13:06-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:47-DEBUG-profile : Using pandas version 0.23.4
+ |-- 11:47-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
+ |-- 11:47-DEBUG-profile : Using numpy version 1.13.3
+ |-- 11:47-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
+ |-- 11:47-DEBUG-profile : Using plotnine version 0.4.0
+ |-- 11:47-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
+ |-- 11:47-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_is7wskbl
+ |-- 11:47-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_is7wskbl/mini_real_promoter
+ |-- 11:47-INFO-profile : Getting configuration info from input file.
+ |-- 11:47-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:47-DEBUG-profile : Color order :[&#39;H3K79me&#39;, &#39;H3K4me3&#39;, &#39;H3K36me3&#39;]
+ |-- 11:47-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
+ |-- 11:47-INFO-profile : Searching coverage columns.
+ |-- 11:47-INFO-profile : Melting.
+ |-- 11:47-INFO-profile : Computing column ordering.
+ |-- 11:47-INFO-profile : Preparing diagram
+ |-- 11:47-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:47-INFO-profile : Preparing x axis
+ |-- 11:47-INFO-profile : facet_col 1
+ |-- 11:47-INFO-profile : Page width set to 3
+ |-- 11:47-INFO-profile : Page height set to 2
+ |-- 11:47-INFO-profile : Saving diagram to file : example_04_max_a.png
+ |-- 11:47-INFO-profile : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 </div></blockquote>
 <a class="reference internal image-reference" href="example_04_max_a.png"><img alt="example_04_max_a.png" src="example_04_max_a.png" style="width: 75%;" /></a>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if example_04_max_b.png  -V 2 -lw 1 -at 5 -s max -ul 0.99
- |-- 13:06-DEBUG-profile : Using pandas version 0.23.4
- |-- 13:06-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
- |-- 13:06-DEBUG-profile : Using numpy version 1.13.3
- |-- 13:06-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
- |-- 13:06-DEBUG-profile : Using plotnine version 0.4.0
- |-- 13:06-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
- |-- 13:06-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_8pslynl6
- |-- 13:06-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_8pslynl6/mini_real_promoter
- |-- 13:06-INFO-profile : Getting configuration info from input file.
- |-- 13:06-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
- |-- 13:06-DEBUG-profile : Color order :[&#39;H3K4me3&#39;, &#39;H3K36me3&#39;, &#39;H3K79me&#39;]
- |-- 13:06-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
- |-- 13:06-INFO-profile : Searching coverage columns.
- |-- 13:06-INFO-profile : Melting.
- |-- 13:06-INFO-profile : Ceiling
- |-- 13:06-INFO-profile : Computing column ordering.
- |-- 13:06-INFO-profile : Preparing diagram
- |-- 13:06-INFO-profile : Theming and ordering. Please be patient...
- |-- 13:06-INFO-profile : Preparing x axis
- |-- 13:06-INFO-profile : facet_col 1
- |-- 13:06-INFO-profile : Page width set to 3
- |-- 13:06-INFO-profile : Page height set to 2
- |-- 13:06-INFO-profile : Saving diagram to file : example_04_max_b.png
- |-- 13:06-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:47-DEBUG-profile : Using pandas version 0.23.4
+ |-- 11:47-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
+ |-- 11:47-DEBUG-profile : Using numpy version 1.13.3
+ |-- 11:47-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
+ |-- 11:47-DEBUG-profile : Using plotnine version 0.4.0
+ |-- 11:47-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
+ |-- 11:47-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_ogporq3f
+ |-- 11:47-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_ogporq3f/mini_real_promoter
+ |-- 11:47-INFO-profile : Getting configuration info from input file.
+ |-- 11:47-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+ |-- 11:47-DEBUG-profile : Color order :[&#39;H3K36me3&#39;, &#39;H3K4me3&#39;, &#39;H3K79me&#39;]
+ |-- 11:47-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
+ |-- 11:47-INFO-profile : Searching coverage columns.
+ |-- 11:47-INFO-profile : Melting.
+ |-- 11:47-INFO-profile : Ceiling
+ |-- 11:47-INFO-profile : Computing column ordering.
+ |-- 11:47-INFO-profile : Preparing diagram
+ |-- 11:47-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:47-INFO-profile : Preparing x axis
+ |-- 11:47-INFO-profile : facet_col 1
+ |-- 11:47-INFO-profile : Page width set to 3
+ |-- 11:47-INFO-profile : Page height set to 2
+ |-- 11:47-INFO-profile : Saving diagram to file : example_04_max_b.png
+ |-- 11:47-INFO-profile : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_04_max_b.png"><img alt="example_04_max_b.png" src="example_04_max_b.png" style="width: 75%;" /></a>
@@ -3336,94 +3341,94 @@ <h3>profile<a class="headerlink" href="#profile" title="Permalink to this headli
 <p>Faceted plot of epigenetic profiles. The groups (i.e colors/lines) can be set to bwig classes and the facets to transcript classes. Things can be simply done by providing an additional file containing the transcript and their associated classes.</p>
 <p><strong>Example:</strong></p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -f tx_classes -g bwig -fo -t tx_classes.txt -o profile_prom  -pf png -if example_05.png -e -V 2 -fc 2
- |-- 13:06-DEBUG-profile : Using pandas version 0.23.4
- |-- 13:06-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
- |-- 13:06-DEBUG-profile : Using numpy version 1.13.3
- |-- 13:06-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
- |-- 13:06-DEBUG-profile : Using plotnine version 0.4.0
- |-- 13:06-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
- |-- 13:06-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_uymw1n8g
- |-- 13:06-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_uymw1n8g/mini_real_promoter
- |-- 13:06-INFO-profile : Getting configuration info from input file.
- |-- 13:06-INFO-profile : Reading transcript file.
- |-- 13:06-INFO-profile : Deleting duplicates in transcript-file.
- |-- 13:06-INFO-profile : Checking how many genes where found in the transcript list.
- |-- 13:06-INFO-profile : Keeping 804 transcript out of 833.
- |-- 13:06-DEBUG-profile : Color order :[&#39;H3K79me&#39;, &#39;H3K36me3&#39;, &#39;H3K4me3&#39;]
- |-- 13:06-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
- |-- 13:06-INFO-profile : Searching coverage columns.
- |-- 13:06-INFO-profile : Melting.
- |-- 13:06-INFO-profile : Ceiling
- |-- 13:06-INFO-profile : Computing column ordering.
- |-- 13:06-INFO-profile : Preparing diagram
- |-- 13:06-INFO-profile : Theming and ordering. Please be patient...
- |-- 13:06-INFO-profile : Preparing x axis
- |-- 13:06-INFO-profile : facet_col 2
- |-- 13:06-INFO-profile : Page width set to 6
- |-- 13:06-INFO-profile : Page height set to 5.0
- |-- 13:06-INFO-profile : Saving diagram to file : example_05.png
- |-- 13:06-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:47-DEBUG-profile : Using pandas version 0.23.4
+ |-- 11:47-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
+ |-- 11:47-DEBUG-profile : Using numpy version 1.13.3
+ |-- 11:47-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
+ |-- 11:47-DEBUG-profile : Using plotnine version 0.4.0
+ |-- 11:47-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
+ |-- 11:47-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_bk158xze
+ |-- 11:47-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_bk158xze/mini_real_promoter
+ |-- 11:47-INFO-profile : Getting configuration info from input file.
+ |-- 11:47-INFO-profile : Reading transcript file.
+ |-- 11:47-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 11:47-INFO-profile : Checking how many genes where found in the transcript list.
+ |-- 11:47-INFO-profile : Keeping 804 transcript out of 833.
+ |-- 11:47-DEBUG-profile : Color order :[&#39;H3K79me&#39;, &#39;H3K4me3&#39;, &#39;H3K36me3&#39;]
+ |-- 11:47-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
+ |-- 11:47-INFO-profile : Searching coverage columns.
+ |-- 11:47-INFO-profile : Melting.
+ |-- 11:47-INFO-profile : Ceiling
+ |-- 11:47-INFO-profile : Computing column ordering.
+ |-- 11:47-INFO-profile : Preparing diagram
+ |-- 11:47-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:47-INFO-profile : Preparing x axis
+ |-- 11:47-INFO-profile : facet_col 2
+ |-- 11:47-INFO-profile : Page width set to 6
+ |-- 11:47-INFO-profile : Page height set to 5.0
+ |-- 11:47-INFO-profile : Saving diagram to file : example_05.png
+ |-- 11:47-INFO-profile : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_05.png"><img alt="example_05.png" src="example_05.png" style="width: 100%;" /></a>
 <p>Alternatively, the groups can be set to chromosomes or transcript classes:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -g tx_classes -f bwig -fo -t tx_classes.txt -o profile_prom  -pf png -if example_06.png -V 2 -nm ranging
- |-- 13:06-DEBUG-profile : Using pandas version 0.23.4
- |-- 13:06-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
- |-- 13:06-DEBUG-profile : Using numpy version 1.13.3
- |-- 13:06-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
- |-- 13:06-DEBUG-profile : Using plotnine version 0.4.0
- |-- 13:06-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
- |-- 13:06-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_c7b7_tvf
- |-- 13:06-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_c7b7_tvf/mini_real_promoter
- |-- 13:06-INFO-profile : Getting configuration info from input file.
- |-- 13:06-INFO-profile : Reading transcript file.
- |-- 13:06-INFO-profile : Deleting duplicates in transcript-file.
- |-- 13:06-INFO-profile : Checking how many genes where found in the transcript list.
- |-- 13:06-INFO-profile : Keeping 804 transcript out of 833.
- |-- 13:06-DEBUG-profile : Color order :[&#39;protein_coding&#39;, &#39;antisense&#39;, &#39;lincRNA&#39;]
- |-- 13:06-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
- |-- 13:06-INFO-profile : Searching coverage columns.
- |-- 13:06-INFO-profile : Melting.
- |-- 13:06-INFO-profile : Ceiling
- |-- 13:06-INFO-profile : Normalizing (ranging)
- |-- 13:06-INFO-profile : Computing column ordering.
- |-- 13:06-INFO-profile : Preparing diagram
- |-- 13:06-INFO-profile : Theming and ordering. Please be patient...
- |-- 13:06-INFO-profile : Preparing x axis
- |-- 13:06-INFO-profile : facet_col 3
- |-- 13:06-INFO-profile : Page width set to 9
- |-- 13:06-INFO-profile : Page height set to 2.0
- |-- 13:06-INFO-profile : Saving diagram to file : example_06.png
- |-- 13:06-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:47-DEBUG-profile : Using pandas version 0.23.4
+ |-- 11:47-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
+ |-- 11:47-DEBUG-profile : Using numpy version 1.13.3
+ |-- 11:47-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
+ |-- 11:47-DEBUG-profile : Using plotnine version 0.4.0
+ |-- 11:47-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
+ |-- 11:47-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_61rt9cn9
+ |-- 11:47-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_61rt9cn9/mini_real_promoter
+ |-- 11:47-INFO-profile : Getting configuration info from input file.
+ |-- 11:47-INFO-profile : Reading transcript file.
+ |-- 11:47-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 11:47-INFO-profile : Checking how many genes where found in the transcript list.
+ |-- 11:47-INFO-profile : Keeping 804 transcript out of 833.
+ |-- 11:47-DEBUG-profile : Color order :[&#39;protein_coding&#39;, &#39;antisense&#39;, &#39;lincRNA&#39;]
+ |-- 11:47-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
+ |-- 11:47-INFO-profile : Searching coverage columns.
+ |-- 11:47-INFO-profile : Melting.
+ |-- 11:47-INFO-profile : Ceiling
+ |-- 11:47-INFO-profile : Normalizing (ranging)
+ |-- 11:47-INFO-profile : Computing column ordering.
+ |-- 11:47-INFO-profile : Preparing diagram
+ |-- 11:47-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:47-INFO-profile : Preparing x axis
+ |-- 11:47-INFO-profile : facet_col 3
+ |-- 11:47-INFO-profile : Page width set to 9
+ |-- 11:47-INFO-profile : Page height set to 2.0
+ |-- 11:47-INFO-profile : Saving diagram to file : example_06.png
+ |-- 11:47-INFO-profile : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_06.png"><img alt="example_06.png" src="example_06.png" style="width: 100%;" /></a>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -g chrom -f bwig -fo -t tx_classes.txt -o profile_prom  -pf png -if example_06b.png -V 2 -nm ranging
- |-- 13:06-DEBUG-profile : Using pandas version 0.23.4
- |-- 13:06-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
- |-- 13:06-DEBUG-profile : Using numpy version 1.13.3
- |-- 13:06-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
- |-- 13:06-DEBUG-profile : Using plotnine version 0.4.0
- |-- 13:06-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
- |-- 13:06-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_r558a_vx
- |-- 13:06-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_r558a_vx/mini_real_promoter
- |-- 13:06-INFO-profile : Getting configuration info from input file.
- |-- 13:06-DEBUG-profile : Color order :[&#39;chr10&#39;, &#39;chr19&#39;, &#39;chr21&#39;, &#39;chr1&#39;, &#39;chrX&#39;, &#39;chr12&#39;, &#39;chr7&#39;, &#39;chr15&#39;, &#39;chr4&#39;, &#39;chr16&#39;, &#39;chr3&#39;, &#39;chr5&#39;, &#39;chr2&#39;, &#39;chr8&#39;, &#39;chr20&#39;, &#39;chr11&#39;, &#39;chr13&#39;, &#39;chr9&#39;, &#39;chr6&#39;, &#39;chr18&#39;, &#39;chr14&#39;, &#39;chr17&#39;, &#39;chr22&#39;]
- |-- 13:06-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#6c007c&#39;, &#39;#850096&#39;, &#39;#2500a5&#39;, &#39;#0000ca&#39;, &#39;#0041dd&#39;, &#39;#0086dd&#39;, &#39;#009fca&#39;, &#39;#00aaa1&#39;, &#39;#00a76f&#39;, &#39;#009c00&#39;, &#39;#00bb00&#39;, &#39;#00da00&#39;, &#39;#00f900&#39;, &#39;#88ff00&#39;, &#39;#dbf400&#39;, &#39;#f7db00&#39;, &#39;#ffb500&#39;, &#39;#ff6100&#39;, &#39;#f60000&#39;, &#39;#da0000&#39;, &#39;#cc1313&#39;, &#39;#cccccc&#39;]
- |-- 13:06-INFO-profile : Searching coverage columns.
- |-- 13:06-INFO-profile : Melting.
- |-- 13:06-INFO-profile : Ceiling
- |-- 13:07-INFO-profile : Normalizing (ranging)
- |-- 13:07-INFO-profile : Computing column ordering.
- |-- 13:07-INFO-profile : Preparing diagram
- |-- 13:07-INFO-profile : Theming and ordering. Please be patient...
- |-- 13:07-INFO-profile : Preparing x axis
- |-- 13:07-INFO-profile : facet_col 3
- |-- 13:07-INFO-profile : Page width set to 9
- |-- 13:07-INFO-profile : Page height set to 2.0
- |-- 13:07-INFO-profile : Saving diagram to file : example_06b.png
- |-- 13:07-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:47-DEBUG-profile : Using pandas version 0.23.4
+ |-- 11:47-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/pandas/__init__.py
+ |-- 11:47-DEBUG-profile : Using numpy version 1.13.3
+ |-- 11:47-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/numpy/__init__.py
+ |-- 11:47-DEBUG-profile : Using plotnine version 0.4.0
+ |-- 11:47-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_py3k/lib/python3.6/site-packages/plotnine/__init__.py
+ |-- 11:47-DEBUG-profile : Uncompressing : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_21k_ugzg
+ |-- 11:47-DEBUG-profile : Reading : /var/folders/nl/stqvvbcn4pg9v65k8kyjv5yh0000gn/T/pygtftk_matrix_21k_ugzg/mini_real_promoter
+ |-- 11:47-INFO-profile : Getting configuration info from input file.
+ |-- 11:47-DEBUG-profile : Color order :[&#39;chr20&#39;, &#39;chr7&#39;, &#39;chr19&#39;, &#39;chr12&#39;, &#39;chrX&#39;, &#39;chr2&#39;, &#39;chr10&#39;, &#39;chr6&#39;, &#39;chr21&#39;, &#39;chr22&#39;, &#39;chr11&#39;, &#39;chr3&#39;, &#39;chr9&#39;, &#39;chr18&#39;, &#39;chr16&#39;, &#39;chr17&#39;, &#39;chr14&#39;, &#39;chr1&#39;, &#39;chr15&#39;, &#39;chr5&#39;, &#39;chr8&#39;, &#39;chr13&#39;, &#39;chr4&#39;]
+ |-- 11:47-DEBUG-profile : Profile color :[&#39;#000000&#39;, &#39;#6c007c&#39;, &#39;#850096&#39;, &#39;#2500a5&#39;, &#39;#0000ca&#39;, &#39;#0041dd&#39;, &#39;#0086dd&#39;, &#39;#009fca&#39;, &#39;#00aaa1&#39;, &#39;#00a76f&#39;, &#39;#009c00&#39;, &#39;#00bb00&#39;, &#39;#00da00&#39;, &#39;#00f900&#39;, &#39;#88ff00&#39;, &#39;#dbf400&#39;, &#39;#f7db00&#39;, &#39;#ffb500&#39;, &#39;#ff6100&#39;, &#39;#f60000&#39;, &#39;#da0000&#39;, &#39;#cc1313&#39;, &#39;#cccccc&#39;]
+ |-- 11:47-INFO-profile : Searching coverage columns.
+ |-- 11:47-INFO-profile : Melting.
+ |-- 11:47-INFO-profile : Ceiling
+ |-- 11:47-INFO-profile : Normalizing (ranging)
+ |-- 11:48-INFO-profile : Computing column ordering.
+ |-- 11:48-INFO-profile : Preparing diagram
+ |-- 11:48-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:48-INFO-profile : Preparing x axis
+ |-- 11:48-INFO-profile : facet_col 3
+ |-- 11:48-INFO-profile : Page width set to 9
+ |-- 11:48-INFO-profile : Page height set to 2.0
+ |-- 11:48-INFO-profile : Saving diagram to file : example_06b.png
+ |-- 11:48-INFO-profile : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_06b.png"><img alt="example_06b.png" src="example_06b.png" style="width: 100%;" /></a>
@@ -3454,7 +3459,7 @@ <h3>profile<a class="headerlink" href="#profile" title="Permalink to this headli
 <p>It is also possible to use several of the previously seen commands to easily achieve more complexe analyses.
 Here we will plot the epigenetic signal according to RNA-seq counts.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk join_attr -i mini_real_noov_rnd_tx.gtf  -j mini_real_counts_ENCFF630HEX.txt  -k gene_name -n counts | gtftk discretize_key -k  counts -n 6 -d count_levels -pu | gtftk tabulate -k transcript_id,count_levels -o tx_exp_classes.txt -Hun
- |-- 13:09-INFO-discretize_key : Categories: [&#39;(-41.703_183.167]&#39;, &#39;(183.167_574.667]&#39;, &#39;(574.667_1035.0]&#39;, &#39;(1035.0_1647.333]&#39;, &#39;(1647.333_3212.667]&#39;, &#39;(3212.667_41703.0]&#39;]
+ |-- 11:50-INFO-discretize_key : Categories: [&#39;(-41.703_183.167]&#39;, &#39;(183.167_574.667]&#39;, &#39;(574.667_1035.0]&#39;, &#39;(1035.0_1647.333]&#39;, &#39;(1647.333_3212.667]&#39;, &#39;(3212.667_41703.0]&#39;]
 </pre></div>
 </div>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_tx.zip -o profile_tx -pf png -if example_12.png  -g tx_classes -t tx_exp_classes.txt -f bwig  -w -nm ranging -m viridis
@@ -3569,11 +3574,13 @@ <h3>control_list<a class="headerlink" href="#control-list" title="Permalink to t
 <p><strong>Description:</strong> Returns a list of gene matched for expression based on reference values. Based on a reference gene list (or more generally IDs) this command tries to extract a set of other genes/IDs matched for signal/expression. The –reference-gene-file contains the list of reference IDs while the –inputfile contains a tuple gene/signal for all genes.</p>
 <p><strong>Example:</strong></p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk control_list -i mini_real_counts_ENCFF630HEX.txt -r mini_real_control_1.txt -D -V 2 -s -l -p 1 -ju -if example_13.png -pf png
- |-- 13:09-INFO-control_list : 0 duplicate lines have been deleted in reference file.
- |-- 13:09-INFO-control_list : Found 220 genes of the reference in the provided signal file
- |-- 13:09-INFO-control_list : All reference genes were found.
- |-- 13:10-INFO-control_list : Saving diagram to file : example_13.png
- |-- 13:10-INFO-control_list : Be patient. This may be long for large datasets.
+ |-- 11:51-INFO-control_list : 0 duplicate lines have been deleted in reference file.
+ |-- 11:51-INFO-control_list : Found 50 genes of the reference in the provided signal file
+ |-- 11:51-INFO-control_list : All reference genes were found.
+ |-- 11:51-INFO-control_list : Searching for genes with matched signal.
+ |-- 11:51-INFO-control_list : Preparing a dataframe for plotting.
+ |-- 11:51-INFO-control_list : Saving diagram to file : example_13.png
+ |-- 11:51-INFO-control_list : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="example_13.png"><img alt="example_13.png" src="example_13.png" style="width: 100%;" /></a>
@@ -3772,7 +3779,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="installation.html" title="Installing pygtftk/gtftk"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/py-modindex.html b/docs/manual/build/html/py-modindex.html
index 3367d678..40ac118e 100644
--- a/docs/manual/build/html/py-modindex.html
+++ b/docs/manual/build/html/py-modindex.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Python Module Index &#8212; gtftk 0.9.2 documentation</title>
+    <title>Python Module Index &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -30,7 +30,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="#" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -119,7 +119,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="#" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/search.html b/docs/manual/build/html/search.html
index d2791bd6..c529b6c6 100644
--- a/docs/manual/build/html/search.html
+++ b/docs/manual/build/html/search.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Search &#8212; gtftk 0.9.2 documentation</title>
+    <title>Search &#8212; gtftk 0.9.3 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -87,7 +87,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
diff --git a/docs/manual/build/html/searchindex.js b/docs/manual/build/html/searchindex.js
index 3f6c64b2..b63eb855 100644
--- a/docs/manual/build/html/searchindex.js
+++ b/docs/manual/build/html/searchindex.js
@@ -1 +1 @@
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pygtftk","Help on Python package (pygtftk)","The gtftk.bam.bam_coverage_matrix module","Writing your own commands","&lt;no title&gt;","Installing pygtftk/gtftk","Help on gtftk Unix commands"],titleterms:{"5p_3p_coord":6,"class":1,The:[1,2],about:0,activ:6,add_exon_nb:6,add_prefix:6,annot:6,apropo:6,argument:6,bam:2,bam_coverage_matrix:2,bash:6,bed_to_gtf:6,closest_gen:6,col_from_tab:6,command:[3,6],complet:6,control_list:6,convent:0,converg:6,convert:6,convert_ensembl:6,coordin:6,count:6,count_key_valu:6,coverag:6,del_attr:6,discretize_kei:6,diverg:6,edit:6,exon_s:6,fasta:1,feature_s:6,file:0,format:0,from:6,funtion:6,get:6,get_attr_list:6,get_attr_value_list:6,get_exampl:6,get_feat_seq:6,get_feature_list:6,get_tx_seq:6,gtf:[0,1],gtftk:[1,2,5,6],help:[1,6],inform:6,instal:5,intergen:6,intron:6,intron_s:6,join_attr:6,join_multi_fil:6,line:1,list:6,main:6,merge_attr:6,midpoint:6,miscellan:6,mk_matrix:6,modul:[1,2],name:0,nb_exon:6,nb_transcript:6,overlap:6,own:3,packag:1,parser:6,profil:6,pygtftk:[0,1,5],python:1,random_list:6,random_tx:6,retriev:6,rm_dup_tss:6,section:6,select:6,select_by_go:6,select_by_intron_s:6,select_by_kei:6,select_by_loc:6,select_by_max_exon_nb:6,select_by_nb_exon:6,select_by_numeric_valu:6,select_by_regexp:6,select_by_tx_s:6,select_most_5p_tx:6,seqid_list:6,sequenc:6,shift:6,short_long:6,splicing_sit:6,support:0,tab:1,tabul:6,test:6,tss_dist:6,unix:6,util:1,warn:0,wide:6,write:3,your:3}})
\ No newline at end of file
diff --git a/docs/manual/source/conf.py b/docs/manual/source/conf.py
index eb885bd2..d11025f8 100644
--- a/docs/manual/source/conf.py
+++ b/docs/manual/source/conf.py
@@ -50,10 +50,10 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.9.2'
+version = u'0.9.3'
 
 # The full version, including alpha/beta/rc tags.
-release = u'0.9.2'
+release = u'0.9.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/pygtftk/cmd_manager.py b/pygtftk/cmd_manager.py
index a93d8a23..eb35d568 100644
--- a/pygtftk/cmd_manager.py
+++ b/pygtftk/cmd_manager.py
@@ -16,13 +16,14 @@
 import tempfile
 import textwrap
 from argparse import Action
+from builtins import object
+from builtins import range
+from builtins import str
 from subprocess import Popen, PIPE
+from sys import platform
 
 import cloudpickle
 import yaml
-from builtins import object
-from builtins import range
-from builtins import str
 
 import pygtftk
 import pygtftk.cmd_object
@@ -99,7 +100,6 @@ def add_parser_group(self, title):
 # An additional action that print Bash completion
 # ---------------------------------------------------------------
 
-
 class BashCompletionAction(argparse._StoreTrueAction):
     """A class to be used by argparser to get bash completion."""
 
@@ -113,6 +113,11 @@ def __call__(self, parser, namespace, values, option_string=None):
         sys.exit()
 
 
+# ---------------------------------------------------------------
+# An additional action that list available plugins
+# ---------------------------------------------------------------
+
+
 class ListPlugins(argparse._StoreTrueAction):
     """A class to be used by argparser to list plugins."""
 
@@ -176,7 +181,11 @@ def __call__(self, parser, namespace, values, option_string=None):
             test = CmdManager.cmd_obj_list[cmd].test
 
             if test is not None and re.search("@test", test):
-                print(test)
+                if platform == "darwin":
+                    print(test)
+                else:
+                    test = test.replace("md5sum-lite", "md5sum")
+                    print(test)
             else:
                 cmd_with_no_test += [cmd]
 
@@ -294,7 +303,41 @@ def __call__(self, parser, namespace, values, option_string=None):
 
 
 # ---------------------------------------------------------------
-# An additional action to install plugins
+# An additional action to get information about the environment
+# ---------------------------------------------------------------
+
+class getSysInfo(argparse._StoreTrueAction):
+    """A class to be used by argparser to get information about the environment."""
+
+    def __init__(self, option_strings, dest, nargs='+', **kwargs):
+        super(getSysInfo, self).__init__(option_strings, dest, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        from pandas import __version__ as pandas_ver
+        from pybedtools import __version__ as pybedtools_ver
+        from pyBigWig import __version__ as pyBigWig_ver
+        from pygtftk import __path__ as pygtftk_path
+        import subprocess
+        from pygtftk.utils import chomp
+        info_sys = []
+        info_sys += ['\n- pygtftk version : ' + __version__]
+        info_sys += ['- pygtftk path : ' + pygtftk_path[0]]
+        info_sys += ['- python version : ' + str(sys.version_info)]
+        info_sys += ['- python path : ' + str(sys.prefix)]
+        info_sys += ['- pandas version : ' + pandas_ver]
+        bedtools_ver = chomp(subprocess.Popen("bedtools --version",
+                                              shell=True,
+                                              stdout=subprocess.PIPE).stdout.read().decode())
+        info_sys += ['- Bedtools version : ' + bedtools_ver]
+        info_sys += ['- pybedtools version : ' + pybedtools_ver]
+        info_sys += ['- pyBigWig version : ' + pyBigWig_ver]
+        info_sys += ['- uname : ' + str(os.uname())]
+        print("\n".join(info_sys))
+        sys.exit()
+
+
+# ---------------------------------------------------------------
+# The cmdManager class
 # ---------------------------------------------------------------
 
 
@@ -330,7 +373,7 @@ class CmdManager(object):
   gtftk select_by_key -k feature -v transcript |   gtftk tabulate -k "*" -b
   
 
-  Use 'gtftk sub-command -h' for more information.
+  Type 'gtftk sub-command -h' for more information.
 
     """
 
@@ -360,6 +403,11 @@ class CmdManager(object):
                         help="Display bats tests for all plugin.",
                         action=GetTests)
 
+    parser.add_argument('-s', '--system-info',
+                        nargs=0,
+                        help="Display some info about the system.",
+                        action=getSysInfo)
+
     if PY3:
         parser.add_argument('-v', '--version',
                             action='version',
@@ -911,7 +959,7 @@ def run(cls, args):
         # Delete arg that won't be used by supparsers
         for key_arg in ['bash_comp', 'add_chr', 'version', 'help',
                         'plugin_tests', 'list_plugins',
-                        'r_libs', 'add_plugin', 'update_plugins']:
+                        'r_libs', 'add_plugin', 'update_plugins', 'system_info']:
             try:
                 del args[key_arg]
             except:
diff --git a/pygtftk/data/__init__.py b/pygtftk/data/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/data/control_list/__init__.py b/pygtftk/data/control_list/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/data/mini_real/__init__.py b/pygtftk/data/mini_real/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/data/mini_real/mini_real_control_1.txt b/pygtftk/data/mini_real/mini_real_control_1.txt
index c57d3f07..63e045ec 100644
--- a/pygtftk/data/mini_real/mini_real_control_1.txt
+++ b/pygtftk/data/mini_real/mini_real_control_1.txt
@@ -48,173 +48,3 @@ PGP	1102
 MINPP1	1744
 AC025165.3	1
 TRAM2-AS1	183
-LATS2	65
-NCLN	2647
-MAGI2	91
-SYTL3	9
-AC097374.1	213
-DUSP18	54
-AC120498.4	7
-GRIN3B	2
-AL691432.2	157
-REV3L-IT1	2
-AC007249.2	97
-TRIM62	31
-AC104333.2	1
-HDHD5	772
-SYNE3	228
-TSPAN4	583
-MIR26B	8
-TRIP12	5776
-AL365226.1	26
-AC004808.2	5
-SENP3	777
-LINC01424	32
-AC126755.1	82
-UBE4A	3289
-BMP8A	5
-MTCYBP18	1
-AC132938.3	12
-SYBU	82
-AC090844.2	6
-RN7SL220P	4
-CCDC84	433
-AC008703.1	1
-RPSAP8	2
-FDPSP5	1
-ZNF283	747
-TMEM170B	16
-SNHG16	7237
-AC017002.6	4
-RNF11	550
-LINC01835	118
-AC005779.1	1
-DCDC1	11
-BCRP8	19
-MISP3	57
-AC107075.1	7
-OFD1	1489
-AC097652.1	3
-CFAP206	1
-RN7SL801P	17
-MED25	754
-LRRC37B	295
-MAML3	40
-AC108516.2	1
-CLECL1	1
-AL356488.3	37
-CYTH4	54
-KHK	279
-EXOC4	4347
-RNU6-5P	1
-SNORD114-14	5
-AC092279.1	58
-SNORA20	51
-AC008741.2	80
-PEX1	1892
-AC025034.1	6
-ERBB4	1
-RPL5P34	16
-WASH2P	175
-ETV2	9
-TBC1D9B	2272
-AC025750.1	1
-RNF26	276
-GPR179	3
-PPP2R5D	1922
-LINC01332	2
-TPX2	7193
-PPP1R2P10	3
-AC010983.1	6
-AC091060.1	25
-POGLUT1	702
-AC135048.4	10
-RPL39L	1053
-ZNF708	267
-AL645608.1	18
-AC026803.2	13
-TMPO	15840
-AL357078.1	3
-SNORD38A	10
-ABCC13	2
-THOC3	860
-LRP4-AS1	10
-RPSAP39	4
-AC135803.1	1
-ELOA-AS1	295
-ARL4AP5	9
-AP001178.1	17
-AL359504.2	122
-TAL1	4786
-NUTM2D	35
-THAP10	2
-GBP5	113
-TRAF7	2681
-OTOG	12
-WDR90	175
-AC015712.2	2
-AL356356.1	12
-APOBEC3G	249
-KLHL15	1084
-L29074.1	1
-AC090922.1	13
-ZCCHC4	702
-LINC02585	3
-TRIM11	2017
-LINC02365	1
-ZNF112	123
-TCAM1P	371
-AC104211.1	344
-PRKCB	14561
-RNU1-18P	2
-KDM1A	9991
-NEMP1	3340
-HIST1H1A	1
-SPATA20	103
-BRD3OS	223
-AC068870.1	2
-RN7SKP102	2
-MEI4	1
-AC243830.2	2
-AC073332.1	17
-EML6	16
-Z98048.1	5
-DNLZ	27
-C11orf98	28
-PCP2	41
-TMEM43	2146
-AC011468.5	38
-WDR82	3159
-LINC01898	1
-PPP1R37	666
-SCRN2	676
-FHL1	16
-LSM2	3361
-IGHE	27
-KLF15	74
-SLC38A2	14279
-AC016526.3	95
-AC005150.1	13
-LY6G6C	4
-MORF4L2-AS1	15
-TAB3	1014
-SNORD53B	12
-GAB1	448
-AL360181.3	2
-CYP1A1	4
-ASMTL-AS1	6
-AC008966.1	114
-GMCL1	1113
-ZNF732	27
-FAM209B	1
-AL122008.3	1
-LINC01202	1
-ZNF514	754
-AC010654.1	23
-AC016734.2	4
-PAFAH1B2	5902
-PRR3	533
-TGOLN2	2775
-SDAD1	1797
-AL590682.1	1
-AC009133.1	15
diff --git a/pygtftk/data/simple_02/__init__.py b/pygtftk/data/simple_02/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/data/simple_03/__init__.py b/pygtftk/data/simple_03/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/data/simple_05/__init__.py b/pygtftk/data/simple_05/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/gtf_interface.py b/pygtftk/gtf_interface.py
index cb7d6b53..3fd38432 100644
--- a/pygtftk/gtf_interface.py
+++ b/pygtftk/gtf_interface.py
@@ -19,13 +19,13 @@
 import re
 import sys
 import textwrap
-from collections import OrderedDict
-from collections import defaultdict
-
 from builtins import object
 from builtins import range
 from builtins import str
 from builtins import zip
+from collections import OrderedDict
+from collections import defaultdict
+
 from cffi import FFI
 from future.utils import native_str
 from pybedtools.bedtool import BedTool
@@ -463,6 +463,8 @@ def __init__(
         else:
             raise GTFtkError("Unsupported input type.")
 
+        message("Instantiating a GTF.")
+
         if new_data is None:
 
             self._data = self._dll.load_GTF(native_str(self.fn))
@@ -590,6 +592,7 @@ def _message(self, msg="", type='DEBUG'):
         >>> a_gtf._message('bla')
         >>> pygtftk.utils.VERBOSITY = 0
         """
+
         addr = re.search("([^\s]+)>", repr(self._data))
         addr = addr.group(1)
 
@@ -603,6 +606,7 @@ def _message(self, msg="", type='DEBUG'):
                              c=addr,
                              d=id(self),
                              e=self._nb)
+
             message(msg, type=type)
 
 
@@ -2406,8 +2410,9 @@ def write(self, output, add_chr=0, gc_off=False):
         >>> assert simple_line_count(b_file) == 70
 
         """
+
         if gc_off:
-            message("Disabling garbage collector.", type="DEBUG")
+            message("Garbage collector has been disabled.", type="DEBUG")
             gc.disable()
 
         self._message("Writing a GTF ")
@@ -2452,7 +2457,8 @@ def write(self, output, add_chr=0, gc_off=False):
 
         if output_str != "-":
             output.close()
-        message("GTF written.")
+
+        self._message("GTF written ")
 
     def get_sequences(self, genome=None, intron=False, rev_comp=True):
         """
diff --git a/pygtftk/plugins/control_list.py b/pygtftk/plugins/control_list.py
index c8179fc8..d4c74d77 100755
--- a/pygtftk/plugins/control_list.py
+++ b/pygtftk/plugins/control_list.py
@@ -338,6 +338,8 @@ def control_list(in_file=None,
 
     nb_candidate_left = exp_data.shape[0] - len(reference_genes_found)
 
+    message("Searching for genes with matched signal.")
+
     if nb_candidate_left < len(reference_genes_found):
         message("Not enough element to perform selection. Exiting", type="ERROR")
 
@@ -346,7 +348,7 @@ def control_list(in_file=None,
         not_candidates = list(set(not_candidates))
 
         diff = abs(exp_data.loc[i] - exp_data)
-        control_list += diff.loc[np.setdiff1d(diff.index, not_candidates)].idxmin(axis=0, skipna=True).tolist()
+        control_list.extend(diff.loc[np.setdiff1d(diff.index, not_candidates)].idxmin(axis=0, skipna=True).tolist())
 
     # -------------------------------------------------------------------------
     #
@@ -354,6 +356,8 @@ def control_list(in_file=None,
     #
     # -------------------------------------------------------------------------
 
+    message("Preparing a dataframe for plotting.")
+
     reference = exp_data_save.loc[reference_genes_found].sort_values('exprs')
     reference = reference.assign(genesets=['Reference'] * reference.shape[0])
 
diff --git a/pygtftk/plugins/convert_ensembl.py b/pygtftk/plugins/convert_ensembl.py
index 9efdb0a0..94d88abe 100644
--- a/pygtftk/plugins/convert_ensembl.py
+++ b/pygtftk/plugins/convert_ensembl.py
@@ -70,7 +70,7 @@ def convert_ensembl(
     gtf = GTF(inputfile,
               check_ensembl_format=False
               ).convert_to_ensembl(check_gene_chr=not no_check_gene_chr,
-                                   ).write(outputfile)
+                                   ).write(outputfile, gc_off=True)
 
     close_properly(outputfile, inputfile)
 
diff --git a/pygtftk/plugins/divergent.py b/pygtftk/plugins/divergent.py
index 2791e32d..6b1df9cc 100644
--- a/pygtftk/plugins/divergent.py
+++ b/pygtftk/plugins/divergent.py
@@ -5,7 +5,6 @@
 import math
 import os
 import sys
-
 from builtins import str
 
 from pygtftk.arg_formatter import FileWithExtension
@@ -205,7 +204,7 @@ def divergent(
 
     else:
         gtf.select_by_key("transcript_id",
-                          ",".join(list(tx_with_divergent.keys()))).write()
+                          ",".join(list(tx_with_divergent.keys()))).write(outputfile, gc_off=True)
 
     close_properly(outputfile, inputfile)
 
diff --git a/pygtftk/plugins/nb_transcripts.py b/pygtftk/plugins/nb_transcripts.py
index df835e6e..97794325 100644
--- a/pygtftk/plugins/nb_transcripts.py
+++ b/pygtftk/plugins/nb_transcripts.py
@@ -4,9 +4,8 @@
 import argparse
 import os
 import sys
-from collections import OrderedDict
-
 from builtins import str
+from collections import OrderedDict
 
 from pygtftk.arg_formatter import FileWithExtension
 from pygtftk.cmd_object import CmdObject
@@ -94,7 +93,7 @@ def nb_transcripts(inputfile=None,
         gtf.add_attr_from_file(feat="gene",
                                key="gene_id",
                                new_key=key_name,
-                               inputfile=tmp_file.name).write(outputfile)
+                               inputfile=tmp_file.name).write(outputfile, gc_off=True)
 
     close_properly(outputfile, inputfile)
 
diff --git a/pygtftk/plugins/overlapping.py b/pygtftk/plugins/overlapping.py
index 43c81138..4f47bb03 100644
--- a/pygtftk/plugins/overlapping.py
+++ b/pygtftk/plugins/overlapping.py
@@ -5,9 +5,8 @@
 import argparse
 import os
 import sys
-from collections import defaultdict
-
 from builtins import str
+from collections import defaultdict
 
 from pygtftk.arg_formatter import FileWithExtension
 from pygtftk.arg_formatter import checkChromFile
@@ -251,7 +250,7 @@ def overlapping(
         values = ",".join(set(overlapping_tx.keys()))
         gtf.select_by_key("transcript_id",
                           values,
-                          invert_match).write(outputfile)
+                          invert_match).write(outputfile, gc_off=True)
 
     close_properly(outputfile, inputfile)
 
diff --git a/pygtftk/plugins/profile.py b/pygtftk/plugins/profile.py
index ef6d8df6..03d707a5 100644
--- a/pygtftk/plugins/profile.py
+++ b/pygtftk/plugins/profile.py
@@ -1160,13 +1160,13 @@ def get_list_of_colors_mpl(number, pal=palette):
                            size=6,
                            ha='left')
 
-        # --------------------------------------------------------------------------
-        #
-        # Apply colors
-        #
-        # --------------------------------------------------------------------------
+    # --------------------------------------------------------------------------
+    #
+    # Apply colors
+    #
+    # --------------------------------------------------------------------------
 
-        p += scale_color_manual(values=dict(list(zip(color_order, profile_colors))), name='Groups')
+    p += scale_color_manual(values=dict(list(zip(color_order, profile_colors))), name='Groups')
 
     # -------------------------------------------------------------------------
     # Turn warning off. Both pandas and plotnine use warnings for deprecated
diff --git a/pygtftk/plugins/random_list.py b/pygtftk/plugins/random_list.py
index 54bfb876..a4464018 100644
--- a/pygtftk/plugins/random_list.py
+++ b/pygtftk/plugins/random_list.py
@@ -5,7 +5,6 @@
 import os
 import random
 import sys
-
 from builtins import str
 
 from pygtftk.arg_formatter import FileWithExtension
@@ -111,7 +110,8 @@ def random_list(
 
     my_id = ft_type + "_id"
 
-    gtf.select_by_key(my_id, ",".join(id_list)).write(outputfile)
+    gtf.select_by_key(my_id, ",".join(id_list)).write(outputfile,
+                                                      gc_off=True)
 
     close_properly(outputfile, inputfile)
 
diff --git a/pygtftk/src/__init__.py b/pygtftk/src/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/src/libgtftk/README.md b/pygtftk/src/libgtftk/README.md
new file mode 100644
index 00000000..bf41da94
--- /dev/null
+++ b/pygtftk/src/libgtftk/README.md
@@ -0,0 +1,27 @@
+# libgtftk README section
+
+Libgtftk is a core library designed to parse and index GTF files. This library provides basic functions to loop through a GTF file efficiently, and to perform basic operations including selecting/subsetting by keys or features, editing/updating key values and more complexe operations at the gene or transcript level such as fetching feature sequences from FASTA files.. This library is intended to be called by external clients written in various languages including C, JAVA, [Python](https://github.com/dputhier/pygtftk), R...  
+
+## System requirements
+
+The libgtftk has been tested on UNIX-like systems including:
+
+ - OSX (10.11.6)
+ - Linux (Ubuntu 12.04, 14.04, 16.04)
+
+
+## Compilation
+
+
+Under Linux:
+
+      git clone https://github.com/dputhier/libgtftk.git
+      cd libgtftk
+      gcc -o libgtftk.so -fPIC *.c command/*.c -I. -lz -shared
+
+Under OSX:
+
+      git clone https://github.com/dputhier/libgtftk.git
+      cd libgtftk
+      gcc -o libgtftk.so -fPIC *.c command/*.c -I. -lz -dynamiclib
+
diff --git a/pygtftk/src/libgtftk/__init__.py b/pygtftk/src/libgtftk/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/src/libgtftk/command/__init__.py b/pygtftk/src/libgtftk/command/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/pygtftk/src/libgtftk/command/add_attr_to_pos.c b/pygtftk/src/libgtftk/command/add_attr_to_pos.c
index 0b0c3f60..6060da2b 100644
--- a/pygtftk/src/libgtftk/command/add_attr_to_pos.c
+++ b/pygtftk/src/libgtftk/command/add_attr_to_pos.c
@@ -18,7 +18,6 @@
 extern GTF_DATA *clone_gtf_data(GTF_DATA *gtf_data);
 extern void add_attribute(GTF_ROW *row, char *key, char *value);
 extern int split_ip(char ***tab, char *s, char *delim);
-extern char *trim_ip(char *);
 
 /*
  * global variables declaration
diff --git a/pygtftk/src/libgtftk/command/convert_to_ensembl.c b/pygtftk/src/libgtftk/command/convert_to_ensembl.c
index c8175630..5812b148 100644
--- a/pygtftk/src/libgtftk/command/convert_to_ensembl.c
+++ b/pygtftk/src/libgtftk/command/convert_to_ensembl.c
@@ -95,9 +95,9 @@ static void action_transcript(const void *nodep, const VISIT which, const int de
 							nbrow++;
 						}
 				}
-				asprintf(&(tr_row->field[3]), "%d", start);
-				asprintf(&(tr_row->field[4]), "%d", end);
-				if (ok) {
+				if (asprintf(&(tr_row->field[3]), "%d", start) > 0 &&
+					asprintf(&(tr_row->field[4]), "%d", end) > 0 &&
+					ok) {
 					if (!strcmp(gtf_d->data[datap->row[0]]->field[2], "gene")) {
 						tr_row->next = gtf_d->data[datap->row[0]]->next;
 						gtf_d->data[datap->row[0]]->next = tr_row;
@@ -186,14 +186,14 @@ static void action_gene(const void *nodep, const VISIT which, const int depth) {
 						}
 					}
 				}
-				asprintf(&(g_row->field[3]), "%d", start);
-				asprintf(&(g_row->field[4]), "%d", end);
-
-				g_row->next = gtf_d->data[datap->row[0]];
-				if (datap->row[0] != 0)
-					gtf_d->data[datap->row[0] - 1]->next = g_row;
-				else
-					gtf_d0 = g_row;
+				if (asprintf(&(g_row->field[3]), "%d", start) > 0 &&
+					asprintf(&(g_row->field[4]), "%d", end) > 0) {
+					g_row->next = gtf_d->data[datap->row[0]];
+					if (datap->row[0] != 0)
+						gtf_d->data[datap->row[0] - 1]->next = g_row;
+					else
+						gtf_d0 = g_row;
+				}
 			}
 			break;
 		case endorder:
diff --git a/pygtftk/src/libgtftk/command/get_sequences.c b/pygtftk/src/libgtftk/command/get_sequences.c
index 6c2e0619..92476232 100644
--- a/pygtftk/src/libgtftk/command/get_sequences.c
+++ b/pygtftk/src/libgtftk/command/get_sequences.c
@@ -188,8 +188,9 @@ FILE *get_fasta_file_index(FILE *fasta_file, char *index) {
 	FILE *ffi = NULL;
 	long pfasta;
 	char *buffer = NULL, *p_end_dir = NULL;
-	int maxLineSize = 0;
+	size_t maxLineSize = 0;
 	size_t size = 0;
+
 	int n;
 	unsigned long old_crc, crc;
 
@@ -215,7 +216,7 @@ FILE *get_fasta_file_index(FILE *fasta_file, char *index) {
 			free(buffer);
 			buffer = NULL;
 		}
-		fprintf(ffi, "%d\n", maxLineSize - 1);
+		fprintf(ffi, "%lu\n", maxLineSize - 1);
 		fprintf(ffi, "%lx\n", crc);
 		fflush(ffi);
 		rewind(ffi);
@@ -249,7 +250,7 @@ FILE *get_fasta_file_index(FILE *fasta_file, char *index) {
 				free(buffer);
 				buffer = NULL;
 			}
-			fprintf(ffi, "%d\n", maxLineSize - 1);
+			fprintf(ffi, "%lu\n", maxLineSize - 1);
 			fprintf(ffi, "%lx\n", crc);
 			fflush(ffi);
 		}
@@ -260,14 +261,15 @@ FILE *get_fasta_file_index(FILE *fasta_file, char *index) {
 }
 
 void print_fasta_sequence(SEQUENCE *seq) {
-	unsigned int k;
+	size_t k;
+	int l;
 	FEATURE *feat;
 
 	fprintf(stdout, "%s\n", seq->header);
 	for (k = 0; k < strlen(seq->sequence); k += 60)
 		fprintf(stdout, "%.60s\n", seq->sequence + k);
-	for (k = 0; k < seq->features->nb; k++) {
-		feat = seq->features->feature[k];
+	for (l = 0; l < seq->features->nb; l++) {
+		feat = seq->features->feature[l];
 		fprintf(stdout, "  %s : %d-%d (%d-%d)\n", feat->name, feat->start, feat->end, feat->tr_start, feat->tr_end);
 	}
 }
diff --git a/pygtftk/src/libgtftk/libgtftk.h b/pygtftk/src/libgtftk/libgtftk.h
index ce070dea..4ea66080 100644
--- a/pygtftk/src/libgtftk/libgtftk.h
+++ b/pygtftk/src/libgtftk/libgtftk.h
@@ -13,7 +13,7 @@
  * to find memory leaks.
  */
 //#define GTFTOOLKIT_DEBUG
-
+#define test 1
 #ifndef GTFTOOLKIT_GTFTK_SRC_LIB_LIBGTFTK_H_
 #define GTFTOOLKIT_GTFTK_SRC_LIB_LIBGTFTK_H_
 #define _GNU_SOURCE
diff --git a/pygtftk/src/libgtftk/libgtftk.h.old b/pygtftk/src/libgtftk/libgtftk.h.old
deleted file mode 100644
index 0df64a40..00000000
--- a/pygtftk/src/libgtftk/libgtftk.h.old
+++ /dev/null
@@ -1,381 +0,0 @@
-/*
- * libgtftk.h
- *
- *  Created on: Jan 10, 2017
- *      Author: fafa
- *
- *  Header file for the gtftk library.
- *  Contains all the structure definitions and the prototype declarations.
- */
-
-/*
- * If this flag is set, the library output a very huge debug information used
- * to find memory leaks.
- */
-//#define GTFTOOLKIT_DEBUG
-
-#ifndef GTFTOOLKIT_GTFTK_SRC_LIB_LIBGTFTK_H_
-#define GTFTOOLKIT_GTFTK_SRC_LIB_LIBGTFTK_H_
-#define _GNU_SOURCE
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <zlib.h>
-#include <search.h>
-#include <string.h>
-#include <errno.h>
-
-/*
- * Debug of memory allocation. Must be linked with libmemory.so shared library.
- * GTFTOOLKIT_DEBUG must be defined.
- */
-#ifdef GTFTOOLKIT_DEBUG
-extern void *F_calloc(int nb, int size, char *file, const char *func, int line);
-extern void *F_realloc(void *ptr, int size, char *file, const char *func, int line);
-extern void F_free(void *ptr, char *file, const char *func, int line);
-extern void *F_malloc(int size, char *file, const char *func, int line);
-#define calloc(nb, size) F_calloc(nb, size, __FILE__, __func__, __LINE__)
-#define realloc(ptr, size) F_realloc(ptr, size, __FILE__, __func__, __LINE__)
-#define malloc(size) F_malloc(size, __FILE__, __func__, __LINE__)
-#define free(p) F_free(p, __FILE__, __func__, __LINE__)
-#endif /* GTFTOOLKIT_DEBUG */
-
-/*
- * constants for transcript selection in select_transcript function
- */
-#define SHORTEST_TRANSCRIPT 1
-#define LONGEST_TRANSCRIPT 2
-#define MOST5P_TRANSCRIPT 3
-
-/*
- * some usefull macros used in get_sequences.c
- */
-#define MIN(x, y) (x <= y ? x : y)
-#define MAX(x, y) (x > y ? x : y)
-#define COMPLEMENT(c) (	c == 'A' ? 'T' : \
-						c == 'a' ? 't' : \
-						c == 'T' ? 'A' : \
-						c == 't' ? 'a' : \
-						c == 'G' ? 'C' : \
-						c == 'g' ? 'c' : \
-						c == 'C' ? 'G' : \
-						c == 'c' ? 'g' : c)
-
-/*
- * This structure describes the input (i.e. a GTF file or a gzipped GTF file).
- * It is created by the get_gtf_reader function in get_reader.c source file.
- * gzFile or plainfile are set depending on the kind of input (gzip or plain).
- * Even if these two elements are exclusive, they are not in an union to be
- * sure to be compatible with the most of native interfaces.
- */
-typedef struct GTF_READER {
-	/*
-	 * The file name with its path (or "-" for standard input)
-	 */
-	char *filename;
-
-	/*
-	 * A boolean to tell if it is a gzipped file
-	 */
-	int gz;
-
-	/*
-	 * The gzip file descriptor
-	 */
-	gzFile gzfile;
-
-	/*
-	 * The plain file descriptor
-	 */
-	FILE *plainfile;
-} GTF_READER;
-
-/*
- * The structure that represents an attribute (key/value) in the last column of
- * a GTF file.
- */
-typedef struct ATTRIBUTE {
-	char *key, *value;
-	struct ATTRIBUTE *next;
-} ATTRIBUTE;
-
-/*
- * A set of ATTRIBUTE
- */
-typedef struct ATTRIBUTES {
-	ATTRIBUTE **attr;
-	int nb;
-} ATTRIBUTES;
-
-
-/*
- * A structure to store a row from a GTF file.
- */
-typedef struct GTF_ROW {
-	/*
-	 * the 8 first fields of a GTF file row
-	 */
-	char **field;
-
-	/*
-	 * the attributes
-	 */
-	ATTRIBUTES attributes;
-
-	/*
-	 * the rank number of the row in the GTF file
-	 */
-	int rank;
-
-	/*
-	 * the link to the next row
-	 */
-	struct GTF_ROW *next;
-
-} GTF_ROW;
-
-/*
- * This is the structure that holds data in GTF format. It is also the
- * structure used as input/output for most of the functions of the library. To
- * start using the library, one must call the load_GTF() function with a GTF
- * file name in parameter and gets a pointer on a GTF_DATA in return. Then, all
- * the other functions must be called with this GTF_DATA pointer as input.
- * Their result can be another GTF_DATA pointer that can be used as input for
- * another function of the library.
- */
-typedef struct GTF_DATA {
-	/*
-	 * the number of rows
-	 */
-	int size;
-
-	/*
-	 * a table of rows
-	 */
-	GTF_ROW **data;
-
-	/*
-	 * the comments at the beginning of the file, started with "##"
-	 */
-
-} GTF_DATA;
-
-/*
- * This structure represents an index on a column, or on an attribute of the
- * last column.
- */
-typedef struct INDEX {
-	/*
-	 * the name of a column (feature, seqid, ...) or of an attribute (gene_id,
-	 * transcript_id, ...)
-	 */
-	char *key;
-
-	/*
-	 * the pointer on a binary tree created with tsearch C function in
-	 * the index_row function in column.c source file. This tree contains
-	 * ROW_LIST elements described later in this file and that contains a
-	 * token and the associated list of row numbers (the rows containing the
-	 * token as the value of the key (a column name or an attribute name).
-	 */
-	void *data;
-
-	/*
-	 * a reference to the GTF_DATA on which the index has been made
-	 */
-	GTF_DATA *gtf_data;
-
-	/*
-	 * a pointer on the next index
-	 */
-	struct INDEX *next;
-
-} INDEX;
-
-/*
- * A structure that contains the information about an index in the column model:
- * the column and the rank as an index can contain several indexes. The index
- * can be accessed as: column[index_id.column]->index[index_id.index_rank]
- */
-typedef struct INDEX_ID {
-	int column;
-	int index_rank;
-} INDEX_ID;
-
-/*
- * This is a structure that modelize a column of a GTF file.
- */
-typedef struct COLUMN {
-	/*
-	 * the rank number of the column
-	 */
-	int num;
-
-	/*
-	 * the column name : seqid, source, feature, start, end, score, strand,
-	 * phase or attributes
-	 */
-	char *name;
-
-	/*
-	 * the default value to print if no value is available (".")
-	 */
-	char *default_value;
-
-	/*
-	 * a linked list of indexes. It contains only one pointer for each column except
-	 * the attributes column for which there is as needed indexes (one can
-	 * index data on several attributes)
-	 */
-	INDEX **index;
-
-	/*
-	 * the number of indexes in the previous table
-	 */
-	int nb_index;
-} COLUMN ;
-
-/*
- * A list of row numbers associated with a token (the values in the 8 first
- * columns or the values associated to an attribute in the last column). This
- * structure is used in the indexes as elements.
- */
-typedef struct ROW_LIST {
-	/*
-	 * the token that is contained in the rows. For example, this can be "gene"
-	 * or "transcript" for an index on the column feature, or "protein_coding"
-	 * and "lincRNA" for an index on the attribute "gene_biotype".
-	 */
-	char *token;
-
-	/*
-	 * the number of rows
-	 */
-	int nb_row;
-
-	/*
-	 * the table of row numbers
-	 */
-	int *row;
-} ROW_LIST;
-
-/*
- * This is a structure that can hold any tabulated text. It is for example the
- * result of extract_data function. All functions that return a RAW_DATA
- * structure are "terminal" functions because this kind of result cannot be the
- * input of another function.
- */
-typedef struct RAW_DATA {
-	/*
-	 * The number of rows and columns
-	 */
-	int nb_rows, nb_columns;
-
-	/*
-	 * The name of the columns
-	 */
-	char **column_name;
-
-	/*
-	 * The data (nb_rows x nb_columns character strings)
-	 */
-	char ***data;
-} RAW_DATA;
-
-/*
- * This structure is used to store a list of strings. Useful as a function
- * return type like get_attribute_list in get_list.c source file. Also used as
- * hashtable elements to discard redundant rows in extract_data.
- */
-typedef struct STRING_LIST {
-	/*
-	 * the strings
-	 */
-	char **list;
-
-	/*
-	 * the size of the previous list
-	 */
-	int nb;
-} STRING_LIST;
-
-/*
- * Used by get_sequences function to modelize exons, introns ...
- */
-typedef struct SEQFRAG {
-	int start, end;
-	char strand;
-} SEQFRAG ;
-
-typedef struct FEATURE {
-	char *name;
-	int start, end, tr_start, tr_end;
-} FEATURE;
-
-typedef struct FEATURES {
-	FEATURE **feature;
-	int nb;
-} FEATURES;
-
-typedef struct SEQUENCE {
-	char *header, *sequence, strand, *seqid, *gene_id, *transcript_id, *gene_name, *gene_biotype;
-	int start, end;
-	FEATURES *features;
-} SEQUENCE;
-
-typedef struct SEQUENCES {
-	int nb;
-	SEQUENCE **sequence;
-} SEQUENCES;
-
-/*
- * Used by get_list function to store an return the results as a matrix of
- * character strings.
- */
-typedef struct TTEXT {
-	int size;
-	char ***data;
-} TTEXT;
-
-/*
- * used by add_exon_number to sort exons by their start value
- */
-typedef struct SORT_ROW {
-	int row;
-	int value;
-} SORT_ROW;
-
-/*
- * Prototypes for the visible functions (callable by external cient)
- */
-GTF_DATA *load_GTF(char *input);
-GTF_DATA *select_by_key(GTF_DATA *gtf_data, char *key, char *value, int not);
-void print_gtf_data(GTF_DATA *gtf_data, char *output, int add_chr);
-GTF_DATA *select_by_transcript_size(GTF_DATA *gtf_data, int min, int max);
-GTF_DATA *select_by_number_of_exon(GTF_DATA *gtf_data, int min, int max);
-GTF_DATA *select_by_genomic_location(GTF_DATA *gtf_data, int nb_loc, char **chr, int *begin_gl, int *end_gl);
-RAW_DATA *extract_data(GTF_DATA *gtf_data, char *key, int base, int uniq);
-void print_raw_data(RAW_DATA *raw_data, char delim, char *output);
-//GTF_DATA *select_transcript(GTF_DATA *gtf_data, int type);
-SEQUENCES *get_sequences(GTF_DATA *gtf_data, char *genome_file, int intron, int rc);
-int free_gtf_data(GTF_DATA *gtf_data);
-int free_raw_data(RAW_DATA *raw_data);
-char *get_memory(long int size);
-int free_mem(char *ptr);
-TTEXT *get_feature_list(GTF_DATA *gtf_data);
-TTEXT *get_seqid_list(GTF_DATA *gtf_data);
-TTEXT *get_attribute_list(GTF_DATA *gtf_data);
-TTEXT *get_attribute_values_list(GTF_DATA *gtf_data, char *attribute);
-GTF_DATA *convert_to_ensembl(GTF_DATA *gtf_data);
-GTF_DATA *add_attributes(GTF_DATA *gtf_data, char *features, char *key, char *new_key, char *inputfile_name);
-GTF_DATA *del_attributes(GTF_DATA *gtf_data, char *features, char *keys);
-GTF_DATA *select_by_positions(GTF_DATA *gtf_data, int *pos, int size);
-GTF_DATA *add_exon_number(GTF_DATA *gtf_data, char *exon_number_field);
-GTF_DATA *add_prefix(GTF_DATA *gtf_data, char *features, char *key, char *txt, int suffix);
-GTF_DATA *merge_attr(GTF_DATA *gtf_data, char *features, char *keys, char *dest_key, char *sep);
-void clear_indexes(void);
-GTF_DATA *add_attr_column(GTF_DATA *gtf_data, char *inputfile_name, char *new_key);
-GTF_DATA *select_transcript2(GTF_DATA *gtf_data, int type);
-int int_array_test(int *pos, int size);
-
-#endif /* GTFTOOLKIT_GTFTK_SRC_LIB_LIBGTFTK_H_ */
diff --git a/pygtftk/src/libgtftk/version.h b/pygtftk/src/libgtftk/version.h
new file mode 100644
index 00000000..1b3cf138
--- /dev/null
+++ b/pygtftk/src/libgtftk/version.h
@@ -0,0 +1 @@
+#define VERSION 0.9.1
diff --git a/pygtftk/utils.py b/pygtftk/utils.py
index 74a0c789..385cd6a8 100644
--- a/pygtftk/utils.py
+++ b/pygtftk/utils.py
@@ -17,8 +17,6 @@
 from subprocess import Popen
 from tempfile import NamedTemporaryFile
 
-import pysam
-import requests
 from future.utils import old_div
 
 import pygtftk
@@ -212,8 +210,7 @@ def get_example_file(datasetname="simple", ext="gtf"):
     Get the path to a gtf file example located in pygtftk library path.
 
     :param datasetname: The name of the dataset. One of 'simple', 'mini_real', 'simple_02, 'simple_03'.
-    :param ext: Extension. For 'simple' dataset, can be one of 'bam', \
-    'bam.bai', 'bw', 'fa', 'fa.fai', 'chromInfo', 'bt*', 'fq', 'gtf' or '.*'.
+    :param ext: Extension. For 'simple' dataset, can be one of 'bw', 'fa', 'fa.fai', 'chromInfo', 'bt*', 'fq', 'gtf' or '.*'.
     :Example:
 
     >>> from pygtftk.utils import get_example_file
@@ -226,6 +223,7 @@ def get_example_file(datasetname="simple", ext="gtf"):
 
     """
 
+    """
     if datasetname == "mini_real" and ext == "bam":
         message("Retrieving BAM file")
         req = requests.get('https://tinyurl.com/y7ael4fo')
@@ -240,6 +238,7 @@ def get_example_file(datasetname="simple", ext="gtf"):
         samfile = pysam.Samfile("ENCFF742FDS_H3K4me3_K562_sub.bam", "rb")
 
         return samfile
+    """
 
     file_path = glob.glob(os.path.join(os.path.dirname(pygtftk.__file__),
                                        'data',
diff --git a/pygtftk/version.py b/pygtftk/version.py
index 51953057..01aacce5 100644
--- a/pygtftk/version.py
+++ b/pygtftk/version.py
@@ -1 +1,2 @@
-__base_version__ = '0.9.2'
+__base_version__='0.9.3'
+__version__='0.9.3'
diff --git a/requirements.txt b/requirements.txt
index cb05ba08..6722582a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,17 +1,17 @@
 scipy >=1.1.0
 pybedtools >=0.7.8
-pysam >=0.9.1.4
 pyyaml >=3.12
 requests >=2.13.0
 cffi >=1.10.0
 pyparsing >=2.2.0
 biopython >=1.69
-matplotlib >=2.0.2
+matplotlib >=2.0.2,<3
 plotnine >=0.4.0
 GitPython >=2.1.8
-argparse
-nose
 cloudpickle >=0.4.0
 ftputil >=3.3.1
 pandas >=0.23.3
-pybigwig >=0.3.10
\ No newline at end of file
+pybigwig >=0.3.12
+setuptools
+argparse
+future
diff --git a/setup.cfg b/setup.cfg
index 7d1892c1..094e0bdc 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,7 +1,11 @@
 [metadata]
-description-file = README.md
-license_file = LICENSE
+name = pygtftk
+version = 0.9.3
+author = D. Puthier and F. Lopez
+author-email = denis.puthier@univ-amu.fr
 
 [egg_info]
 tag_build =
 tag_date = 0
+
+[bdist_wheel]
diff --git a/setup.py b/setup.py
index 56d951f6..2c94f5ed 100644
--- a/setup.py
+++ b/setup.py
@@ -1,12 +1,10 @@
 """
-The gtfk package.
+The pygtfk package.
 
-The Python GTF toolkit (pygtftk) package is intented to ease handling of GTF (Gene Transfer Format) files. The pygtftk package is compatible with Python 2.7 and relies on libgtftk, a library of functions written in C.
+The Python GTF toolkit (pygtftk) package is intented to ease handling of GTF (Gene Transfer Format) files. The pygtftk package relies on libgtftk, a library of functions written in C.
 The package comes with a set of UNIX commands that can be accessed through the gtftk program. The gtftk program proposes several atomic tools to filter, convert, or extract data from GTF files. The gtftk set of Unix commands can be easily extended using a basic plugin architecture. All these aspects are covered in the help section.
-While the gtftk Unix program comes with hundreds of unitary and functional tests, it is still upon active development and may thus suffer from bugs that remain to be discovered. Feel free to post any problem or required enhancement in the issue section of the github repository.
 
 Authors: D. Puthier and F. Lopez
-Programming Language :: Python :: 2.7"
 """
 
 # -------------------------------------------------------------------------
@@ -30,13 +28,13 @@
     from setuptools import setup
     from setuptools import Extension
 except ImportError:
-    sys.stderr.write("Please install setuptools before installing pygtftk.")
+    sys.stderr.write("Please install setuptools before installing pygtftk.\n")
     exit(1)
 
 try:
     import git
 except ImportError:
-    sys.stderr.write("Please install git package before installing pygtftk.")
+    sys.stderr.write("Please install GitPython package before installing pygtftk.\n")
     exit(1)
 
 # -------------------------------------------------------------------------
@@ -74,7 +72,7 @@
 except:
     sha = ""
 
-if sha != "" and branch != "master" and not os.path.exists("pypi_release_in_progress"):
+if sha != "" and branch != "master" and not os.path.exists("release_in_progress"):
     __version__ = base_version + ".dev0+" + sha
 else:
     __version__ = base_version
@@ -92,40 +90,21 @@
 cmd_src_list += glob.glob("pygtftk/src/libgtftk/command/*.c")
 cmd_src_list = list(set(cmd_src_list))
 
-for i in cmd_src_list:
-    print(i)
-
-if PY2:
-    if platform == "darwin":
-        vars = sysconfig.get_config_vars()
-        vars['LDSHARED'] = vars['LDSHARED'].replace('-bundle', '-dynamiclib')
-        dyn_lib_compil = []
-    else:
-        dyn_lib_compil = []
-
-    extra_compile_args = ['-Ipygtftk/src/libgtftk',
-                          '-O3',
-                          '-Wall',
-                          '-fPIC',
-                          '-MMD',
-                          '-MP',
-                          '-fmessage-length=0'] + dyn_lib_compil
-elif PY3:
-    if platform == "darwin":
-        vars = sysconfig.get_config_vars()
-        vars['LDSHARED'] = vars['LDSHARED'].replace('-bundle', '-dynamiclib')
-        dyn_lib_compil = []
-    else:
-        dyn_lib_compil = []
-
-    extra_compile_args = ['-Ipygtftk/src/libgtftk',
-                          '-O3',
-                          '-Wall',
-                          '-fPIC',
-                          '-fcommon',
-                          '-MMD',
-                          '-MP',
-                          '-fmessage-length=0'] + dyn_lib_compil
+if platform == "darwin":
+    vars = sysconfig.get_config_vars()
+    # vars['LDSHARED'] = vars['LDSHARED'].replace('-bundle', '-dynamiclib')
+    # dyn_lib_compil = ['-dynamiclib', '-shared']
+    dyn_lib_compil = []
+else:
+    dyn_lib_compil = ['-shared']
+
+extra_compile_args = ['-Ipygtftk/src/libgtftk',
+                      '-O3',
+                      '-Wall',
+                      '-fPIC',
+                      '-MMD',
+                      '-MP',
+                      '-fmessage-length=0'] + dyn_lib_compil
 
 lib_pygtftk = Extension(name='pygtftk/lib/libgtftk',
                         include_dirs=[
@@ -150,11 +129,15 @@
 markup_level = 0
 past_line_len = 0
 
+start_of_text = False
+
 for pos, line in enumerate(long_description_file):
     if not line.startswith("    "):
         line = line.rstrip('\r\n')
+    if line.startswith("# ") and start_of_text is False:
+        start_of_text = True
 
-    if pos > 0:
+    if start_of_text:
         # Replace title
         if markup_level > 0:
             title = markup_char[markup_level] * past_line_len
@@ -215,7 +198,7 @@
 
 setup(name="pygtftk",
       version=__version__,
-      author_email='fabrice.lopez@inserm.fr,denis.puthier@univ-amu.fr',
+      author_email='denis.puthier@univ-amu.fr',
       author="fabrice Lopez,Denis Puthier",
       description="The Python GTF toolkit (pygtftk) package: easy handling of GTF files",
       url="https://github.com/dputhier/pygtftk",
@@ -228,6 +211,10 @@
       keywords="genomics bioinformatics GTF BED",
       packages=['pygtftk',
                 'pygtftk/plugins',
+                'docs',
+                'docs/manual',
+                'docs/manual/build',
+                'docs/manual/build/html',
                 'pygtftk/bwig',
                 'pygtftk/rtools',
                 'pygtftk/data',
@@ -252,7 +239,8 @@
                     'pygtftk/plugins': ['*.*'],
                     'pygtftk/src': ['*.*'],
                     'pygtftk/src/libgtftk': ['*.*'],
-                    'pygtftk/src/libgtftk/command': ['*.*']},
+                    'pygtftk/src/libgtftk/command': ['*.*'],
+                    'docs/manual/build/html': ['*.*']},
       scripts=['bin/gtftk'],
       license='LICENSE.txt',
 
@@ -262,6 +250,7 @@
                    "Development Status :: 4 - Beta",
                    "Environment :: Console",
                    "Programming Language :: Python :: 2.7",
+                   "Programming Language :: Python :: 3.5",
                    "Programming Language :: Python :: 3.6",
                    "Programming Language :: Python :: 3.7",
                    "Intended Audience :: Science/Research",
@@ -278,16 +267,17 @@
                         'ftputil >=3.3.1',
                         'pybedtools >=0.7.8',
                         'pandas >=0.23.3',
-                        'pyBigWig >=0.2.8',
                         'requests >=2.13.0',
+                        'pyBigWig >=0.3.12',
                         'cffi >=1.10.0',
                         'biopython >=1.69',
                         'pyparsing >=2.2.0',
                         'GitPython >=2.1.8',
                         'pyparsing',
-                        'pysam >=0.9.1.4',
                         'matplotlib >=2.0.2',
-                        'plotnine >=0.4.0'],
+                        'plotnine >=0.4.0',
+                        'future',
+                        'setuptools'],
       ext_modules=[lib_pygtftk])
 
 config_dir = os.path.join(os.path.expanduser("~"), ".gtftk")