Merge branch 'release_v0.3.3'

CHANGELOG.txt

@@ -1,3 +1,8 @@
+v0.3.3 (2014-07-20)
+- Fix bug in mapping stats table generation
+- Add further mapping success value (use reads that are long enogh
+  after read processing as reference)
+- Improve Makefile
 v0.3.2 (2014-07-12)
 - Add quality trimming and adapter clipping (for reviewer Matt
   MacManes)

Makefile

@@ -45,6 +45,8 @@ 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"
 	@echo "* Change bin/reademption"
 	@echo "* Change setup.py"
 	@echo "* Change docs/source/conf.py"

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__ = "0.3.2"
+__version__ = "0.3.3"
 
 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 = '0.3.2'
+release = '0.3.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

reademptionlib/readalignerstatstable.py

@@ -43,8 +43,10 @@ def _add_global_countings(self):
              self._total_alignment_stat_numbers("no_of_alignments")),
             ("Total no. of split alignments", 
              self._total_alignment_stat_numbers("no_of_split_alignments")),
-            ("Percentage of aligned reads (compared to total input reads)",
-             self._perc_aligned_reads()),
+            ("Percentage of aligned reads (compared to no. of input reads)",
+             self._perc_aligned_reads_all_input()),
+            ("Percentage of aligned reads (compared to no. of long enough reads)",
+             self._perc_aligned_reads_all_long_enough()),
             ("Percentage of uniquely aligned reads (in relation to all aligned "
              "reads)", self._perc_uniquely_aligned_reads())]:
             self._table.append([title] + data)
@@ -84,13 +86,21 @@ def _get_read_process_numbers(self, attribute):
         return [self._read_processing_stats[lib][attribute]
                 for lib in self._libs]
 
-    def _perc_aligned_reads(self):
+    def _perc_aligned_reads_all_input(self):
         return [
             round(self._calc_percentage(aligned_reads, total_reads), 2)
             for aligned_reads, total_reads in
             zip(self._total_alignment_stat_numbers(
                     "no_of_aligned_reads", round_nums=False),
                 self._get_read_process_numbers("total_no_of_reads"))]
+
+    def _perc_aligned_reads_all_long_enough(self):
+        return [
+            round(self._calc_percentage(aligned_reads, total_reads), 2)
+            for aligned_reads, total_reads in
+            zip(self._total_alignment_stat_numbers(
+                    "no_of_aligned_reads", round_nums=False),
+                self._get_read_process_numbers("long_enough"))]
 
     def _perc_uniquely_aligned_reads(self):
         return [

reademptionlib/readprocessor.py

@@ -92,6 +92,7 @@ def _process_single_end(self, input_fh, output_fh):
             if clipped_seq_len < self._min_read_length:
                 self._stats["too_short"] += 1
                 continue
+            self._stats["long_enough"] += 1
             self._stats["read_length_before_processing_and_freq"][
                 raw_seq_len] += 1
             self._stats["read_length_after_processing_and_freq"][

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.3.2',
+    version='0.3.3',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',