Merge branch 'release_v0.3.5'

CHANGELOG.txt

@@ -1,3 +1,9 @@
+v0.3.5 (2015-01-13)
+- Update some pysam related function due to changes in API changes of pysam
+- Add further requirements (matplotlib, Biopython, pandas)
+- Reimplement MA plot generation
+- Add strand-unspecific coverage calculation
+- Several small code improvements
 v0.3.4 (2014-08-23)
 - Fix bug with paired-end suffix
 - Fix bug with paired-end mapping stats table

Makefile

@@ -2,11 +2,16 @@ test:
 	python3 tests/test_all.py
 
 coverage:
-	coverage3 run tests/test_all.py
-	coverage3 report
+	python3-coverage run tests/test_all.py
+	python3-coverage report
 
 package:
 	python3 setup.py sdist
+	rm -rf READemption.egg-info
+	ls dist/*
+
+build:
+	python3 setup.py bdist
 
 package_to_pypi:
 	python3 setup.py sdist upload

bin/reademption

@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2014 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.3.4"
+__version__ = "0.3.5"
 
 def main():
     parser = argparse.ArgumentParser()
@@ -126,6 +126,11 @@ def main():
         "--skip_read_count_splitting", "-s", default=False,
         action="store_true", help="Do not split the read counting between "
         "different alignings. Default is to do the splitting.")
+    coverage_creation_parser.add_argument(
+        "--non_strand_specific", "-d", default=False,
+        action="store_true", help="Do not distict between the coverage of the "
+        "forward and reverse strand but sum them to a single value for each "
+        "base.")
     coverage_creation_parser.add_argument(
         "--first_base_only", "-b", default=False,
         action="store_true", help="Only the first bases 5' base of each read "
@@ -230,6 +235,12 @@ def main():
         "project_path", default=".", nargs="?",
         help="Path of the project folder. If none is given the current "
         "directory is used.")
+
+    viz_deseq_parser.add_argument(
+        "--max_pvalue", type=float, default="0.05",
+        help="Maximum adjusted p-value for genes considered to be regulated. "
+        "Genes with adjusted p-values below will be marked red. "
+        "(default 0.05)")
     viz_deseq_parser.set_defaults(func=viz_deseq)
 
     args = parser.parse_args()

docs/source/conf.py

@@ -50,7 +50,7 @@
 # The short X.Y version.
 version = '0.3'
 # The full version, including alpha/beta/rc tags.
-release = '0.3.4'
+release = '0.3.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/subcommands.rst

@@ -179,6 +179,10 @@ positions. To turn off this behavior use
     --skip_read_count_splitting, -s
                           Do not split the read counting between different
                           alignings. Default is to do the splitting.
+    --non_strand_specific, -d
+                          Do not distict between the coverage of the forward and
+                          reverse strand but sum them to a single value for each
+                          base.
     --first_base_only, -b
                           Only the first bases 5' base of each read aligning is
                           taken into account.
@@ -250,7 +254,7 @@ deseq
 -----
 
 Differential gene expression can be performed using ``deseq`` which
-will run a `DESeq2 <http://www-huber.embl.de/users/anders/DESeq2/>`_
+will run a `DESeq2 <http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html>`_
 analyses for all possible combinations of conditions. To allocated the
 conditions to the libraries use the ``--libs`` and ``--conditions``
 parameters (e.g. ``--libs
@@ -332,3 +336,7 @@ vs. p-values / adjusted p-values).
 
   optional arguments:
     -h, --help    show this help message and exit
+  --max_pvalue MAX_PVALUE
+                          Maximum adjusted p-value for genes considered to be
+                          regulated. Genes with adjusted p-values below will be
+                          marked red. (default 0.05)

reademptionlib/bammerger.py

@@ -2,6 +2,7 @@
 import sys
 import pysam
 
+
 class BamMerger(object):
 
     def merge(self, output_bam, input_bam_1, input_bam_2):