Merge branch 'release/1.2.2' into 'release/1.2'

Merge release/1.2.2 into release/1.2



See merge request !20

Author: emarinier

CHANGELOG.md

@@ -2,6 +2,17 @@
 
 All notable changes to Neptune will be documented in this file.
 
+## [1.2.2] - 2016-04-06
+
+This release includes some Galaxy improvements and fixes a signature scoring
+problem.
+
+### Changed
+- Galaxy XML files have been updated to use different packages of Python.
+
+### Fixed
+- A bug confusing inclusion and exclusion has been fixed.
+
 ## [1.2.1] - 2016-03-23
 
 This release of Neptune adds support for Galaxy.

README.md

@@ -38,11 +38,12 @@ probabilistic models instead of heuristic strategies.
 ## Release ##
 -------------
 
-**Neptune 1.2.1**
+**Neptune 1.2.2**
 
-2016 March 23
+2016 April 6
 
-This release of Neptune adds support for Galaxy.
+This release includes some Galaxy improvements and fixes a signature scoring
+problem.
 
 ## Requirements ##
 ------------------

documentation/manual/Manual.pdf

@@ -64,7 +64,7 @@
 \setlength{\parskip}{0.5em}
 
 %opening
-\title{Neptune\\ \normalsize Version 1.2.1}
+\title{Neptune\\ \normalsize Version 1.2.2}
 \author{Eric Marinier}
 
 \begin{document}
@@ -179,7 +179,7 @@ \subsection{Neptune Installation}
 
 # Ensure installation was successful:
 $ neptune --version
-> neptune 1.2.1
+> neptune 1.2.2
 \end{lstlisting}
 
 \newpage

documentation/manual/Manual.tex

@@ -1,14 +1,18 @@
-<tool id="neptune" name="Neptune: Signature Discovery" version="1.2.1">
+<tool id="neptune" name="Neptune: Signature Discovery" version="1.2.2.0">
   <description>Neptune identifies genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.</description>
 
   <requirements>
-    <requirement type="package" version="1.2.1">neptune</requirement>
-    <requirement type="package" version="1.64">biopython</requirement>
+    <requirement type="package" version="1.2.2">neptune</requirement>
+    <requirement type="package" version="1.66">biopython</requirement>
     <requirement type="package" version="2.2.28">blast+</requirement>
     <requirement type="package" version="1.9">numpy</requirement>
     <requirement type="package" version="0.14">scipy</requirement>
   </requirements>
 
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+
   <command>
     Neptune.py
 

galaxy/neptune/neptune.xml

@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="neptune" version="1.2.1">
+  <package name="neptune" version="1.2.2">
       <repository name="package_neptune" owner="nml" prior_installation_required="True"/>
     </package>
-    <package name="biopython" version="1.64">
-      <repository name="package_biopython_1_64" owner="biopython" prior_installation_required="True"/>
+    <package name="biopython" version="1.66">
+      <repository name="package_python_2_7_biopython_1_66" owner="ulfschaefer" prior_installation_required="True"/>
     </package>
     <package name="numpy" version="1.9">
       <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True"/>
     </package>
     <package name="scipy" version="0.14">
-      <repository name="package_scipy_0_14" owner="iuc" prior_installation_required="True"/>
+      <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True"/>
     </package>
     <package name="blast+" version="2.2.28">
       <repository name="package_blast_plus_2_2_28" owner="iuc" prior_installation_required="True" />

galaxy/neptune/tool_dependencies.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 
 <tool_dependency>
-    <package name="neptune" version="1.2.1">
+    <package name="neptune" version="1.2.2">
         <install version="1.0">
 
             <actions>
@@ -60,11 +60,12 @@ probabilistic models instead of heuristic strategies.
 ## Release ##
 -------------
 
-**Neptune 1.2.1**
+**Neptune 1.2.2**
 
-2016 March 23
+2016 April 6
 
-This release of Neptune adds support for Galaxy.
+This release includes some Galaxy improvements and fixes a signature scoring
+problem.
 
 ## Running Neptune ##
 ---------------------

galaxy/package_neptune/tool_dependencies.xml

@@ -160,8 +160,9 @@ def __init__(
 
         self.filterLength = filterLength            # The min filtering size.
 
-        self.hitOverallDictionary = {}  # The best (hit.ID, X).
-        self.hitPairDictionary = {}     # The best (hit.ID, hit.reference).
+        self.exclusionOverallDictionary = {}        # The best (hit.ID, X).
+        self.inclusionPairDictionary = {}  # The best (hit.ID, hit.reference).
+        self.exclusionPairDictionary = {}  # The best (hit.ID, hit.reference).
 
         self.overallScore = {}          # The overall score of a signature.
         self.inclusionScore = {}        # The inclusion score of a signature.
@@ -184,14 +185,14 @@ def __init__(
         [NONE]
 
     POST:
-        The [self.overallScore] dictionary will be updated.
+        The [self.exclusionOverallDictionary] dictionary will be updated.
 
     # =========================================================================
     """
-    def updateHitOverallDictionary(self, hit):
+    def updateExclusionOverallDictionary(self, hit):
 
-        key = hit.ID                                # The key: ID of the hit.
-        dictionary = self.hitOverallDictionary      # The dictionary to update.
+        key = hit.ID
+        dictionary = self.exclusionOverallDictionary
 
         if key not in dictionary:
 
@@ -204,11 +205,11 @@ def updateHitOverallDictionary(self, hit):
     """
     # =========================================================================
 
-    UPDATE HIT PAIR DICTIONARY
+    UPDATE PAIR DICTIONARY
 
     PURPOSE:
-        The pair score dictionary will be updated with the passed hit. This
-        function is looking for the best hit for a (hit, reference) pair.
+        The passed pair score dictionary will be updated with the passed hit.
+        This function is looking for the best hit for a (hit, reference) pair.
 
     INPUT:
         [HIT] [hit] - The hit object associated with the hit.
@@ -217,14 +218,13 @@ def updateHitOverallDictionary(self, hit):
         [NONE]
 
     POST:
-        The [self.hitPairDictionary] object will be updated.
+        The passed dictionary object will be updated.
 
     # =========================================================================
     """
-    def updateHitPairDictionary(self, hit):
+    def updatePairDictionary(self, dictionary, hit):
 
         key = (hit.ID, hit.reference)           # The key: ID and reference.
-        dictionary = self.hitPairDictionary     # The dictionary to update.
 
         if key not in dictionary:
 
@@ -257,13 +257,13 @@ def updateHitPairDictionary(self, hit):
     POST:
         The exclusion scores and negative component of the overall scores of
         [self.overallScore] and [self.exclusionScore] will be updated using the
-        [self.hitPairDictionary].
+        [self.exclusionPairDictionary].
 
     # =========================================================================
     """
     def updateExclusionScores(self):
 
-        dictionary = self.hitPairDictionary     # The pair dictionary.
+        dictionary = self.exclusionPairDictionary     # The pair dictionary.
 
         for key in dictionary:
 
@@ -302,13 +302,13 @@ def updateExclusionScores(self):
     POST:
         The exclusion scores and negative component of the overall scores of
         [self.overallScore] and [self.inclusionScore] will be updated using the
-        [self.hitPairDictionary].
+        [self.inclusionPairDictionary].
 
     # =========================================================================
     """
     def updateInclusionScores(self):
 
-        dictionary = self.hitPairDictionary     # The pair dictionary.
+        dictionary = self.inclusionPairDictionary     # The pair dictionary.
 
         for key in dictionary:
 
@@ -355,7 +355,7 @@ def reportFilteredCandidates(self):
         outputFile = open(self.filteredLocation, 'w')   # The output.
         candidateSignatures = Signature.readSignatures(
             self.candidatesLocation)                    # The input.
-        dictionary = self.hitOverallDictionary          # Overall dictionary.
+        dictionary = self.exclusionOverallDictionary    # Overall dictionary.
 
         for ID in candidateSignatures:
 
@@ -460,8 +460,8 @@ def reportSignatures(self, exclusionQueryLocation):
         for line in exclusionQueryFile:
 
             hit = Database.Hit(line)
-            self.updateHitOverallDictionary(hit)
-            self.updateHitPairDictionary(hit)
+            self.updateExclusionOverallDictionary(hit)
+            self.updatePairDictionary(self.exclusionPairDictionary, hit)
 
         exclusionQueryFile.close()
 
@@ -498,7 +498,7 @@ def sortSignatures(self, inclusionQueryLocation):
         for line in inclusionQueryFile:
 
             hit = Database.Hit(line)
-            self.updateHitPairDictionary(hit)
+            self.updatePairDictionary(self.inclusionPairDictionary, hit)
 
         inclusionQueryFile.close()
 

neptune/FilterSignatures.py

@@ -26,7 +26,7 @@
 # =============================================================================
 """
 
-__version__ = '1.2.1'
+__version__ = '1.2.2'
 
 import os
 import argparse

neptune/Neptune.py

@@ -5,7 +5,7 @@
 
 setup(
     name='neptune',
-    version='1.2.1',
+    version='1.2.2',
     url='https://github.com/phac-nml/neptune.git',
     license='Apache-2.0',
     author='Eric Marinier',