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Some docstring updates #95

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merged 6 commits into from Nov 26, 2012
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7 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
"""
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4 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.
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12 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.
"""
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4 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
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2 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:
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