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Nicolas MAILLET
rpg
Commits
8b92e569
Commit
8b92e569
authored
Apr 30, 2018
by
Nicolas MAILLET
Browse files
change miss-cleavage to miscleavage
parent
c201c0a3
Changes
1
Hide whitespace changes
Inline
Side-by-side
rpg/digest.py
View file @
8b92e569
...
...
@@ -35,7 +35,7 @@ class ResultOneDigestion:
:param enzyme_name: name of the enzyme used
:param peptides: all resulting peptides after digestion
:param nb_cleavage: number of cleavage that occurs
:param pos_miss_cleavage: position of mis
s-
cleavage that occurs
:param pos_miss_cleavage: position of miscleavage that occurs
:type enzyme_name: str
:type peptides: list(:py:class:`~rpg.sequence.Peptide`)
:type nb_cleavage: int
...
...
@@ -55,10 +55,10 @@ class ResultOneDigestion:
# self representation for print
def
__repr__
(
self
):
return
"Number of cleavage: "
+
str
(
self
.
nb_cleavage
)
+
\
"
\n
Number of mis
s-
cleavage: "
+
\
"
\n
Number of miscleavage: "
+
\
str
(
len
(
self
.
pos_miss_cleavage
))
+
\
"
\n
Positions of mis
s-
cleavage: "
+
str
(
self
.
pos_miss_cleavage
)
\
+
"
\n
Ratio of mis
s-
cleavage: "
+
\
"
\n
Positions of miscleavage: "
+
str
(
self
.
pos_miss_cleavage
)
\
+
"
\n
Ratio of miscleavage: "
+
\
str
(
self
.
get_ratio_miss_cleavage
())
+
\
"
\n
Peptides: "
+
str
(
self
.
peptides
)
+
"
\n
"
...
...
@@ -102,26 +102,26 @@ class ResultOneDigestion:
self
.
nb_cleavage
+=
1
def
get_nb_miss_cleavage
(
self
):
"""Get the number of mis
s-
cleavages that occurs
"""Get the number of miscleavages that occurs
on this digestion.
:return: number of mis
s-
cleavage
:return: number of miscleavage
:rtype: int
"""
return
len
(
self
.
pos_miss_cleavage
)
def
add_miss_cleavage
(
self
,
new_pos_miss_cleavage
):
"""Add a mis
s-
cleavage to :attr:`self.pos_miss_cleavage`.
"""Add a miscleavage to :attr:`self.pos_miss_cleavage`.
:param new_pos_miss_cleavage: position of mis
s-
cleavage
:param new_pos_miss_cleavage: position of miscleavage
:type new_pos_miss_cleavage: int
"""
self
.
pos_miss_cleavage
.
append
(
new_pos_miss_cleavage
)
def
get_ratio_miss_cleavage
(
self
):
"""Get ratio of mis
s-
cleavage.
"""Get ratio of miscleavage.
:return: ratio of mis
s-
cleavage
:return: ratio of miscleavage
:rtype: float
"""
ret
=
0
...
...
@@ -132,9 +132,9 @@ class ResultOneDigestion:
return
ret
def
get_miss_cleavage_pos
(
self
):
"""Get positions of mis
s-
cleavage as a string.
"""Get positions of miscleavage as a string.
:return: positions of mis
s-
cleavage
:return: positions of miscleavage
:rtype: str
"""
ret
=
""
...
...
@@ -186,7 +186,7 @@ class ResultOneDigestion:
def
get_more_info
(
self
):
"""Return informations and statistics about this digestion,
*i.e.* number of (miss)-cleavages and positions, mis
s-
cleavage
*i.e.* number of (miss)-cleavages and positions, miscleavage
ratio, size of the smallest peptide and first and last peptide.
:return: informations and statistics ready to be printed
...
...
@@ -195,10 +195,10 @@ class ResultOneDigestion:
ret
=
""
ret
+=
"
\n
Number of cleavage: "
+
str
(
self
.
nb_cleavage
)
+
"
\n
"
ret
+=
"Cleavage position: "
+
self
.
get_cleavage_pos
()
+
"
\n
"
ret
+=
"Number of mis
s-
cleavage: "
+
str
(
self
.
get_nb_miss_cleavage
())
\
ret
+=
"Number of miscleavage: "
+
str
(
self
.
get_nb_miss_cleavage
())
\
+
"
\n
"
ret
+=
"
M
is
s-
cleavage position: "
+
self
.
get_miss_cleavage_pos
()
+
"
\n
"
ret
+=
"
M
is
s-
cleavage ratio: %.2f%%
\n
"
%
self
.
get_ratio_miss_cleavage
()
ret
+=
"
m
iscleavage position: "
+
self
.
get_miss_cleavage_pos
()
+
"
\n
"
ret
+=
"
m
iscleavage ratio: %.2f%%
\n
"
%
self
.
get_ratio_miss_cleavage
()
ret
+=
"Smallest peptide size: "
+
\
str
(
self
.
get_smallest_peptide
().
size
)
+
"
\n
"
ret
+=
"N terminal peptide: "
+
self
.
peptides
[
0
].
sequence
+
"
\n
"
...
...
@@ -250,9 +250,9 @@ def one_digest(pep, enz):
for
rul
in
enz
.
rules
:
# Apply the rule: if we need to cut
if
rule
.
handle_rule
(
pep
.
sequence
,
pos
,
rul
,
cut
):
# Random to handle mis
s-
cleavage
# Random to handle miscleavage
tmp_rand
=
random
.
random
()
*
100
# Rand > ratio_miss_cleavage, no mis
s-
cleavage occurs
# Rand > ratio_miss_cleavage, no miscleavage occurs
if
tmp_rand
>
enz
.
ratio_miss_cleavage
:
# Test, this should NEVER be used
if
rul
.
pos
==
-
1
:
...
...
@@ -283,7 +283,7 @@ def one_digest(pep, enz):
a_cut_occurs
=
True
# A cleavage occur
ret
.
inc_nb_cleavage
()
# A mis
s-
cleavage occurs
# A miscleavage occurs
else
:
ret
.
add_miss_cleavage
(
pos
)
# End of the peptide
...
...
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