Some docstring updates

Bio/Align/Applications/_ClustalOmega.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # Copyright 2011 by Andreas Wilm. All rights reserved.
 # Based on ClustalW wrapper copyright 2009 by Cymon J. Cox.
 #
@@ -32,11 +33,11 @@ class ClustalOmegaCommandline(AbstractCommandline):
 
     Citation:
 
-    Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R,
-    McWilliam H, Remmert R, Soding J, Thompson JD Higgins DG
+    Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R,
+    McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011).
     Fast, scalable generation of high-quality protein multiple
     sequence alignments using Clustal Omega.
-    Molecular Systems Biology 2011; accepted. 
+    Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75
 
     Last checked against versions: 1.1.0
     """

Bio/Graphics/__init__.py

@@ -4,7 +4,7 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 ################################################################################
-"""Bio.Graphics offsers several graphical outputs, all using ReportLab."""
+"""Bio.Graphics offers several graphical outputs, all using ReportLab."""
 
 # Check if ReportLab is installed.
 try:
@@ -21,7 +21,7 @@
 # code to deal with the different ReportLab renderers
 # and the API quirks consistently.
 def _write(drawing, output_file, format, dpi=72):
-    """Helper function to standize output to files (PRIVATE).
+    """Helper function to standardize output to files (PRIVATE).
 
     Writes the provided drawing out to a file in a prescribed format.
 

Bio/HMM/DynamicProgramming.py

@@ -5,12 +5,12 @@
 """
 
 class AbstractDPAlgorithms(object):
-    """An abstract class to calculate forward and backward probabiliies.
+    """An abstract class to calculate forward and backward probabilities.
 
     This class should not be instantiated directly, but should be used
     through a derived class which implements proper scaling of variables.
 
-    This class is just meant to encapsulate the basic foward and backward
+    This class is just meant to encapsulate the basic forward and backward
     algorithms, and allow derived classes to deal with the problems of
     multiplying probabilities.
 
@@ -23,7 +23,7 @@ class AbstractDPAlgorithms(object):
     step using some technique to prevent underflow errors.
     """
     def __init__(self, markov_model, sequence):
-        """Initialize to calculate foward and backward probabilities.
+        """Initialize to calculate forward and backward probabilities.
 
         Arguments:
 
@@ -42,12 +42,12 @@ def _foward_recursion(self, cur_state, sequence_pos, forward_vars):
     def forward_algorithm(self):
         """Calculate sequence probability using the forward algorithm.
 
-        This implements the foward algorithm, as described on p57-58 of
+        This implements the forward algorithm, as described on p57-58 of
         Durbin et al.
 
         Returns:
 
-        o A dictionary containing the foward variables. This has keys of the
+        o A dictionary containing the forward variables. This has keys of the
         form (state letter, position in the training sequence), and values
         containing the calculated forward variable.
 
@@ -161,7 +161,7 @@ class ScaledDPAlgorithms(AbstractDPAlgorithms):
     manageable numerical interval during calculations. This approach is
     described in Durbin et al. on p 78.
 
-    This approach is a little more straightfoward then log transformation
+    This approach is a little more straightforward then log transformation
     but may still give underflow errors for some types of models. In these
     cases, the LogDPAlgorithms class should be used.
     """

Bio/HotRand.py

@@ -3,7 +3,9 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-"""handles true random numbers supplied from the the web server of fourmilab. Based on atmospheric noise.  The motivation is to support biosimulations that rely on random numbers.
+"""handles true random numbers supplied from the the web server of
+   fourmilab. Based on atmospheric noise.  The motivation is to
+   support biosimulations that rely on random numbers.
 """
 
 import urllib

Bio/Motif/Applications/_AlignAce.py

@@ -8,7 +8,7 @@
 
 AlignACE homepage:
 
-http://atlas.med.harvard.edu/
+http://arep.med.harvard.edu/mrnadata/mrnasoft.html
 
 AlignACE Citations: