Merge branch 'release_v0.3.4'

CHANGELOG.txt

@@ -1,3 +1,8 @@
+v0.3.4 (2014-08-23)
+- Fix bug with paired-end suffix
+- Fix bug with paired-end mapping stats table
+- Add Docker documentation
+- Update reference
 v0.3.3 (2014-07-20)
 - Fix bug in mapping stats table generation
 - Add further mapping success value (use reads that are long enogh

Makefile

@@ -42,8 +42,6 @@ pylint:
 	pylint bin/reademption reademptionlib/* tests/*
 
 new_release:
-	@echo "* Please do this manually:"
-	@echo "* ------------------------"
 	@echo "* Create/checkout a release branch"
 	@echo "  git branch release_v0.3.X"
 	@echo "  git checkout release_v0.3.X"

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__ = "0.3.3"
+__version__ = "0.3.4"
 
 def main():
     parser = argparse.ArgumentParser()

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 = '0.3.3'
+release = '0.3.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/docker_image.rst

@@ -0,0 +1,35 @@
+Docker image
+============
+
+`Docker <https://docker.com/>`_ is a light-weight way to deploy
+applications. We offer an `image for READemption
+<https://registry.hub.docker.com/u/konradfoerstner/reademption/>`_
+that can be easily retrieved and used once you have `Docker installed
+<https://docs.docker.com/installation/>`_. To get the image run
+
+::
+
+  $ sudo docker pull konradfoerstner/reademption
+
+Now you have the image READempmtion image and should see it shown
+in your list of docker images:
+
+::
+
+  $ sudo docker images
+  REPOSITORY                    TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
+  reademption_0.3.3             latest              416dbb001c6b        2 weeks ago         802.5 MB
+  konradfoerstner/reademption   0.3.3               416dbb001c6b        2 weeks ago         802.5 MB
+  ubuntu                        14.04               ba5877dc9bec        4 weeks ago         192.7 MB
+  ubuntu                        latest              ba5877dc9bec        4 weeks ago         192.7 MB
+
+You can simply start the contains by running the following command:
+
+:: 
+
+  $ sudo docker run -i -t reademption_0.3.3 
+  root@3b9e7fd860ee:/# reademption -v
+  READemption version 0.3.3
+
+Inside of this environment you have access to the local installation
+of READemption.

docs/source/index.rst

@@ -8,8 +8,9 @@ Table of content
 
    index
    installation
-   live_and_installation_image      
-   subcommands      
+   live_and_installation_image
+   docker_image
+   subcommands
    example_analysis
    troubleshooting
    license
@@ -50,13 +51,13 @@ Cite
 ====
 
 If you apply READemption in your data analysis please cite the
-following reference: *READemption – A tool for the computational
+following publication: *READemption – A tool for the computational
 analysis of deep-sequencing-based transcriptome data*.
-Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma; (submitted). 
-
-..  A
-.. `pre-preprint version <http://biorxiv.org/content/early/2014/XXX>`_ of
-..  the manuscript is hosted at bioRxiv.
+Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma. 2014,
+Bioinformatics, Aug 13. `Fulltext
+<http://bioinformatics.oxfordjournals.org/content/early/2014/08/13/bioinformatics.btu533.abstract>`_,
+`Pre-print at bioRxiv
+<http://biorxiv.org/content/early/2014/05/19/003723>`_.
 
 Contact
 =======

docs/source/installation.rst

@@ -133,7 +133,7 @@ Install ``matplotlib``:
   pip3 install python3-matplotlib
 
 
-1. Installing segemehl, DESeq, pysam and READemption
+2. Installing segemehl, DESeq, pysam and READemption
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The remaining installation steps are the same as descibed above. Just

reademptionlib/controller.py

@@ -425,7 +425,7 @@ def _write_alignment_stat_table(self):
         read_aligner_stats_table = ReadAlignerStatsTable(
             read_processing_stats, final_alignment_stats, primary_aligner_stats, 
             realignment_stats, self._lib_names, 
-            self._paths.read_alignment_stats_table_path)
+            self._paths.read_alignment_stats_table_path, self._args.paired_end)
         read_aligner_stats_table.write()
 
     def _ref_ids_to_file(self, ref_seq_paths):

reademptionlib/paths.py

@@ -178,14 +178,15 @@ def get_lib_names_paired_end(self):
                    for file_name in self.get_read_files()][::2]
         for p1_name in p1_names:
             if not p1_name.endswith("_p1"):
-                sys.error.write("Error: File '%s' should end with '_p1' but "
+                sys.stderr.write("Error: File '%s' should end with '_p1' but "
                                 "does not. Please check file name convention "
                                 "for paired end reads.\n" % p1_name)
                 sys.exit(1)
         return [p1_name[:-3] for p1_name in p1_names]
 
     def _clean_file_name(self, file_name):
-        for suffix in ["bz2", "BZ", "gz", "GZ", "fa", "fasta", "FA", "FASTA"]:
+        for suffix in ["bz2", "BZ", "gz", "GZ", "fa", "fasta", "FA", "FASTA", 
+                       "fastq", "fq", "FQ", "FASTQ"]:
             if file_name.endswith(suffix):
                 suffix = "." + suffix
                 file_name = file_name[:-len(suffix)]

reademptionlib/readalignerstatstable.py

@@ -1,14 +1,16 @@
 class ReadAlignerStatsTable(object):
 
     def __init__(self, read_processing_stats, alignment_stats, 
-                 primary_read_aligner_stats, realigner_stats, libs, output_path):
+                 primary_read_aligner_stats, realigner_stats, libs, output_path,
+                 paired_end):
         self._table = []
         self._read_processing_stats = read_processing_stats
         self._alignment_stats = alignment_stats
         self._primary_read_aligner_stats = primary_read_aligner_stats
         self._realigner_stats = realigner_stats
         self._libs = libs
         self._output_path = output_path
+        self._paired_end = paired_end
 
     def write(self):
         self._add_global_countings()
@@ -83,7 +85,10 @@ def _total_alignment_stat_numbers(self, attribute, round_nums=True):
             return countings
 
     def _get_read_process_numbers(self, attribute):
-        return [self._read_processing_stats[lib][attribute]
+        factor = 1
+        if self._paired_end:
+            factor = 2
+        return [self._read_processing_stats[lib][attribute] * factor
                 for lib in self._libs]
 
     def _perc_aligned_reads_all_input(self):

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.3.3',
+    version='0.3.4',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',