Set version to 2.0.1

CHANGELOG.txt

@@ -1,3 +1,6 @@
+v2.0.1 (2022-08-23)
+- Accelerate fragment building for paired-end reads
+- Set color blind friendly colors for viz align plots
 v2.0.0 (2022-06-28)
 - Added multi-species analysis (changes the API)
 - Results of subcommands separated by species

CITATION.cff

@@ -13,9 +13,9 @@ authors:
   - family-names: Tobin
     given-names: Diarmaid         
 title: "READemption"
-version: 2.0.0
+version: 2.0.1
 doi: https://zenodo.org/record/6772669
-date-released: 2022-06-28
+date-released: 2022-08-23
 preferred-citation:
   type: article
   authors:
@@ -36,4 +36,8 @@ preferred-citation:
   title: "READemption—a tool for the computational analysis of deep-sequencing–based transcriptome data"
   issue: 23
   volume: 30
+<<<<<<< HEAD
   year: 2014
+=======
+  year: 2014
+>>>>>>> dev

bin/reademption

@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>, Till Sauerwein <sauerwein
 __copyright__ = "2011-2022 by Konrad Foerstner <[email protected], , Till Sauerwein <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected], [email protected]"
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 
 
 def main():

docs/build/html/.buildinfo

@@ -0,0 +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: 583e472278924fbeadb4a0128b32f285
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/installation.rst.txt

@@ -0,0 +1,193 @@
+Installation and updating
+=========================
+
+Requirements
+------------
+
+READemption was started to be developed using Python 3.2 and the user
+is advised to run READemption with this or a higher version. In any
+case `setuptools <https://pypi.python.org/pypi/setuptools>`_ and `pip
+<http://www.pip-installer.org>`_ should be available on the system in
+order to make the installation easy. READemption uses the short read
+mapper `segemehl
+<http://www.bioinf.uni-leipzig.de/Software/segemehl/>`_ for the
+mapping and this software needs to be installed. The subcommands
+``viz_align``, ``viz_gene_quanti``, ``viz_deseq`` require the Python
+library `Matplotlib <http://matplotlib.org/>`_. `R
+<http://www.r-project.org/>`_ and the bioconductor package `DESeq2
+<http://bioconductor.org/packages/release/bioc/html/DESeq2.html>`_ are
+necessary for the subcommand ``deseq`` which performs differential
+gene expression analysis. Don't worry - in the following the
+installation of all these requirements will be covered.
+
+Installing on a fresh Ubuntu system
+-----------------------------------
+
+
+1. Installing all required Debian/Ubuntu packages
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Before starting it is a good idea to update the package list::
+
+  sudo apt-get update
+
+Now you can install the packages::
+
+  sudo apt-get install python3 python3-setuptools python3-pip python3-matplotlib cython3 zlib1g-dev  make libncurses5-dev r-base libxml2-dev
+
+Some comments:
+
+- Python version 3.6 and higher is recommended
+- ``cython`` is required for ``pysam``
+- ``make``, ``libncurses5-dev`` and ``zlib1g-dev`` are needed for ``segemehl``
+- ``libxml2`` is required for the installation of some of the R-packages
+
+2. Install segemehl
+~~~~~~~~~~~~~~~~~~~
+
+::
+
+  curl https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/segemehl-0.3.4.tar.gz > segemehl-0.3.4.tar.gz
+  tar segemehl-0.3.4.tar.gz
+  cd segemehl_*/segemehl*/ && make all && cd ../../
+
+
+Copying the executable to a location that is part of the ``PATH`` e.g
+``/usr/bin/`` ...
+
+::
+  sudo cp segemehl-0.3.4/segemehl-0.3.4/segemehl.x /usr/bin/segemehl.x
+
+... or the bin folder of your home directory::
+
+  mkdir ~/bin
+  cp segemehl-0.3.4/segemehl-0.3.4/segemehl.x ~/bin
+
+
+Alternatively, segemehl can be installed via conda::
+
+  conda install -c bioconda segemehl
+
+
+3. Install DESeq2
+~~~~~~~~~~~~~~~~~
+
+Start ``R``::
+
+  R
+
+
+and install the DESeq2 package inside of the interactive command line
+interface. You might be asked to confirm the installation path::
+
+  source("http://bioconductor.org/biocLite.R")
+  biocLite("DESeq2")
+
+Leave ``R``::
+
+  quit(save = "no")
+
+
+Install  READemption and it's dependcies
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Now you can use ``pip`` to install ``READemption`` and further python
+packages::
+
+  sudo pip3 install READemption
+
+Voilà! You should now be able to call READemption::
+
+  reademption -h
+
+
+Installing on a Apple OS X
+--------------------------
+
+(Many thanks to Lei Li for contribution this part!)
+
+1. Installing all required software/packages
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To download and install Python 3 follow the instruction at this
+`download page <https://www.python.org/downloads/>`_.
+
+Download and install `xcode <https://developer.apple.com/xcode/>`_ (`page <https://developer.apple.com/xcode/downloads/>`_) and R
+(download links are on `the frontpage <http://www.r-project.org/>`_).
+
+To install ``pip`` open a terminal and run
+
+::
+
+  curl -O https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py python3 ez_setup.py # download and install pip 
+  curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py 
+  python3 get-pip.py
+
+Install ``matplotlib``:
+
+::
+
+  pip3 install matplotlib
+
+
+2. Installing segemehl, DESeq, pysam and READemption
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The remaining installation steps are the same as descibed above. Just
+open a terminal and run the commands.
+
+
+Updating READemption
+--------------------
+
+Once you have installed READemption as described above you can easily
+upgrade it to the newest version by running
+
+::
+
+  pip3 install --upgrade READemption
+
+
+Package version requirements and installation
+---------------------------------------------
+Create a python version 3.9 environment
+::
+    conda create --name py3.9_reademption python=3.9
+
+Activate the environment
+::
+    conda activate py3.9_reademption
+
+Install pysam
+::
+    conda install -c bioconda pysam=0.19.1
+
+
+Install segemehl
+::
+    conda install -c bioconda segemehl=0.3.4
+
+Install biopython (numpy 1.23 included)
+
+::
+    conda install biopython=1.79
+
+Install pandas
+
+::
+    conda install pandas=1.4.3
+
+Install seaborn
+
+::
+    conda install seaborn=0.11.2
+
+Install matplotlib
+
+::
+    conda install matplotlib=3.5.2
+
+Install pytest (only required for testing)
+
+::
+    conda install pytest

docs/build/html/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,134 @@
+/*
+ * _sphinx_javascript_frameworks_compat.js
+ * ~~~~~~~~~~
+ *
+ * Compatability shim for jQuery and underscores.js.
+ *
+ * WILL BE REMOVED IN Sphinx 6.0
+ * xref RemovedInSphinx60Warning
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}