Merge branch 'dev'

CHANGELOG.txt

@@ -1,4 +1,7 @@
-v0.3.8 (2016-03-07)
+v0.4.0 (2016-07-27)
+- Fix issue with pysam in samtobam.py
+- Update installation documentation
+v0.3.9 (2016-03-07)
 - Add support for centered approach in coverage and gene_quanti
   (by Thorsten Bischler)
 - Fix bar chart creation in viz_gene_quanti (by Thorsten Bischler)

Makefile

@@ -11,10 +11,10 @@ package:
 	ls dist/*
 
 build:
-	python3 setup.py bdist
+	python3 setup.py bdist_wheel
 
 package_to_pypi:
-	python3 setup.py sdist upload
+	python3 setup.py bdist_wheel upload
 	@echo "Go to https://pypi.python.org/pypi/READemption/"
 
 html_doc:
@@ -48,8 +48,8 @@ pylint:
 
 new_release:
 	@echo "* Create/checkout a release branch"
-	@echo "  git branch release_v0.3.X"
-	@echo "  git checkout release_v0.3.X"
+	@echo "  git branch release_v0.4.X"
+	@echo "  git checkout release_v0.4.X"
 	@echo "* Change bin/reademption"
 	@echo "* Change setup.py"
 	@echo "* Change docs/source/conf.py"
@@ -59,8 +59,8 @@ new_release:
 	@echo "* Test doc creation"
 	@echo "* make package_to_pypi"
 	@echo "* git add CHANGELOG.txt bin/reademption docs/source/conf.py setup.py"
-	@echo "* Commit changes e.g. 'git commit -m \"Set version to 0.3.X\"'"
-	@echo "* Tag the commit e.g. 'git tag -a v0.3.X -m \"version v0.3.X\"'"
+	@echo "* Commit changes e.g. 'git commit -m \"Set version to 0.4.X\"'"
+	@echo "* Tag the commit e.g. 'git tag -a v0.4.X -m \"version v0.4.X\"'"
 	@echo "* Merge release into dev and master"
 	@echo "* Push it to github: git push"
 	@echo "* Generate a new release based on this tag at"

bin/reademption

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""READemption - A RNA-seq Analysis PipeLine"""
+"""READemption - A RNA-seq Analysis Pipeline"""
 
 import argparse
 from reademptionlib.controller import Controller
@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2016 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.3.9"
+__version__ = "0.4.0"
 
 
 def main():

docs/source/conf.py

@@ -41,16 +41,16 @@
 
 # General information about the project.
 project = u'READemption'
-copyright = u'2015, Konrad U. Förstner'
+copyright = u'2016, Konrad U. Förstner'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.3'
+version = '0.4'
 # The full version, including alpha/beta/rc tags.
-release = '0.3.9'
+release = '0.4.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/installation.rst

@@ -6,9 +6,7 @@ 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, the third party packages `Biopython <http://biopython.org>`_,
-`pysam <https://code.google.com/p/pysam>`_ as well as `setuptools
-<https://pypi.python.org/pypi/setuptools>`_ and `pip
+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
@@ -44,32 +42,32 @@ Now you can install the packages::
 
 Some comments:
 
-- Ubuntu 14.04 should have Python 3.4 already installed.
+- Ubuntu 16.04 should have Python 3.5 already installed.
 - ``cython`` is required for ``pysam``
 - ``make``, ``libncurses5-dev`` and ``zlib1g-dev`` are needed for ``segemehl``
-- ``libxml2`` required for the installation of some of the R-packages
+- ``libxml2`` is required for the installation of some of the R-packages
 
 2. Install segemehl
 ~~~~~~~~~~~~~~~~~~~
 
 ::
 
-  curl http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_0_1_9.tar.gz > segemehl_0_1_9.tar.gz
-  tar xzf segemehl_0_1_9.tar.gz
+  curl http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_0_2_0.tar.gz > segemehl_0_2_0.tar.gz
+  tar xzf segemehl_0_2_0.tar.gz
   cd segemehl_*/segemehl/ && make && cd ../../
 
 Copying the executable to a location that is part of the ``PATH`` e.g
 ``/usr/bin/`` ...
 
 ::
 
-  sudo cp segemehl_0_1_9/segemehl/segemehl.x /usr/bin/segemehl.x
-  sudo cp segemehl_0_1_9/segemehl/lack.x /usr/bin/lack.x
+  sudo cp segemehl_0_2_0/segemehl/segemehl.x /usr/bin/segemehl.x
+  sudo cp segemehl_0_2_0/segemehl/lack.x /usr/bin/lack.x
 
 ... or the bin folder of your home directory::
 
   mkdir ~/bin
-  cp segemehl_0_1_9/segemehl/segemehl.x ~/bin
+  cp segemehl_0_2_0/segemehl/segemehl.x ~/bin
 
 3. Install DESeq2
 ~~~~~~~~~~~~~~~~~
@@ -90,13 +88,12 @@ Leave ``R``::
   quit(save = "no")
 
 
-Install Biopython, pysam and READemption
+Install  READemption and it's dependcies
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Now you can use ``pip`` to install ``pysam`` and ``READemption``::
+Now you can use ``pip`` to install ``READemption`` and further python
+packages::
 
-  sudo pip3 install biopython
-  sudo pip3 install pysam
   sudo pip3 install READemption
 
 Voilà! You should now be able to call READemption::
@@ -130,7 +127,7 @@ Install ``matplotlib``:
 
 ::
 
-  pip3 install python3-matplotlib
+  pip3 install matplotlib
 
 
 2. Installing segemehl, DESeq, pysam and READemption
@@ -144,8 +141,8 @@ Updating READemption
 --------------------
 
 Once you have installed READemption as described above you can easily
-update it to the newest version by running
+upgrade it to the newest version by running
 
 ::
 
-  pip3 install READemption -U
+  pip3 install --upgrade READemption

reademptionlib/sambamconverter.py

@@ -19,7 +19,13 @@ def sam_to_bam(self, sam_path, bam_path_prefix):
         temp_unsorted_bam_path = self._temp_unsorted_bam_path(
             bam_path_prefix)
         # Generate unsorted BAM file
-        pysam.view("-Sb", "-o%s" % temp_unsorted_bam_path, sam_path)
+        #### The following line does not work since pysam 0.9.1.4:
+        #### pysam.view("-Sb", "-o%s" % temp_unsorted_bam_path, sam_path)
+        ####
+        #### This is nasty, hopefully only temporaly work-around:
+        with open(temp_unsorted_bam_path, "wb") as unsorted_bam_fh:
+            bam_content = pysam.view("-Sb", sam_path)
+            unsorted_bam_fh.write(bam_content)
         # Generate sorted BAM file
         pysam.sort(temp_unsorted_bam_path, "-o", bam_path_prefix + ".bam")
         # Generate index for BAM file

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.3.9',
+    version='0.4.0',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',