Merge branch 'dev'

CHANGELOG.txt

@@ -1,3 +1,5 @@
+v0.4.2 (2016-08-29)
+- Replace ugly pysam view construct (thanks to Thorsten Bischler)
 v0.4.1 (2016-08-02)
 - Fix another issue with pysam in samtobam.py
 - Update dependencies

Makefile

@@ -55,6 +55,7 @@ new_release:
 	@echo "* Change docs/source/conf.py"
 	@echo "* Change CHANGELOG.txt"
 	@echo "* Create new docs"
+	@echo "  make html_doc"
 	@echo "* Test package creation"
 	@echo "* Test doc creation"
 	@echo "* make package_to_pypi"

bin/reademption

@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2016 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.4.1"
+__version__ = "0.4.2"
 
 
 def main():

docs/source/conf.py

@@ -50,7 +50,7 @@
 # The short X.Y version.
 version = '0.4'
 # The full version, including alpha/beta/rc tags.
-release = '0.4.1'
+release = '0.4.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

reademptionlib/sambamconverter.py

@@ -19,13 +19,9 @@ 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
-        #### 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)
+        pysam.samtools.view(
+            "-b", "-o{}".format(temp_unsorted_bam_path), sam_path,
+            catch_stdout=False)
         # Generate sorted BAM file
         pysam.sort(temp_unsorted_bam_path, "-o", bam_path_prefix + ".bam")
         # Generate index for BAM file
@@ -36,11 +32,7 @@ def sam_to_bam(self, sam_path, bam_path_prefix):
         os.remove(sam_path)
 
     def bam_to_sam(self, bam_path, sam_path):
-        #### Same problem as above!!!
-        # pysam.view("-ho%s" % sam_path, bam_path)
-        with open(sam_path, "w") as sam_fh:
-            sam_content = pysam.view("-h", bam_path,)
-            sam_fh.write(sam_content)
+        pysam.view("-ho{}".format(sam_path), bam_path, catch_stdout=False)
 
     def _temp_unsorted_bam_path(self, bam_path_prefix):
         return "%s%s.bam" % (bam_path_prefix, self._unsorted_appendix)

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.4.1',
+    version='0.4.2',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',