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Fix more typos.

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commit 902947a7df49d8529faeb7e1bfb55b2d06252272 1 parent c6a4f14
@cbrueffer cbrueffer authored
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4 Bio/Pathway/__init__.py
@@ -21,7 +21,7 @@
Network.
The Bio.Pathway classes, especially Interaction, are intentionally
-desgined to be very flexible. Their intended use are as wrappers around database
+designed to be very flexible. Their intended use are as wrappers around database
specific records, such as BIND objects. The value-added in this module is a
framework for representing collections of reactions in a way that supports
graph theoretic and numeric analysis.
@@ -221,7 +221,7 @@ def stochiometry(self):
class Interaction(object):
"""An arbitrary interaction between any number of species.
- This class definition is inteded solely as a minimal wrapper interface that should
+ This class definition is intended solely as a minimal wrapper interface that should
be implemented and extended by more specific abstractions.
Attributes:
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6 Bio/SubsMat/MatrixInfo.py
@@ -18,9 +18,9 @@
'pam90', 'rao', 'risler', 'structure'
]
-#NOTE - The only reason we define temp functions rather than assinging
-#the dictionaries directly to variables is too work arround a JVM
-#limitation on code size if runnning under Jython. The temp functions
+#NOTE - The only reason we define temp functions rather than assigning
+#the dictionaries directly to variables is to work around a JVM
+#limitation on code size if running under Jython. The temp functions
#have an underscore to indicate they are private, and are in any case
#deleted after use (partly to ensure we don't use any of them twice).
View
8 Bio/SubsMat/__init__.py
@@ -19,7 +19,7 @@
which are the two residue/nucleotide types replaced. The value differs
according to the matrix's purpose: e.g in a log-odds frequency matrix, the
value would be log(Pij/(Pi*Pj)) where:
-Pij: frequency of substitution of letter (residue/nucletide) i by j
+Pij: frequency of substitution of letter (residue/nucleotide) i by j
Pi, Pj: expected frequencies of i and j, respectively.
Usage:
@@ -42,7 +42,7 @@
As order doesn't matter, user can already provide only one entry:
['A','C']: 22
A SeqMat instance may be initialized with either a full (first
-method of counting: 10, 12) or half (the latter method, 22) matrices. A
+method of counting: 10, 12) or half (the latter method, 22) matrix. A
Full protein alphabet matrix would be of the size 20x20 = 400. A Half
matrix of that alphabet would be 20x20/2 + 20/2 = 210. That is because
same-letter entries don't change. (The matrix diagonal). Given an
@@ -50,7 +50,7 @@
Full matrix size:N*N
Half matrix size: N(N+1)/2
-If you provide a full matrix, the constructore will create a half-matrix
+If you provide a full matrix, the constructor will create a half-matrix
automatically.
If you provide a half-matrix, make sure of a (low, high) sorted order in
the keys: there should only be
@@ -541,7 +541,7 @@ def two_mat_relative_entropy(mat_1,mat_2,logbase=2,diag=diagALL):
if i in key_list_2:
key_list.append(i)
if len(key_list_1) != len(key_list_2):
- sys.stderr.write("Warning:first matrix has more entries than the second\n")
+ sys.stderr.write("Warning: first matrix has more entries than the second\n")
if key_list_1 != key_list_2:
sys.stderr.write("Warning: indices not the same between matrices\n")
for key in key_list:
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