From 0f5fa6f7e7537fdb98236331efc4b22edb36bcb4 Mon Sep 17 00:00:00 2001
From: Nicolas MAILLET <nicolas.maillet@pasteur.fr>
Date: Wed, 16 May 2018 16:51:50 +0200
Subject: [PATCH] Correct bug when several rules apply at same time
---
rpg/digest.py | 7 ++++---
rpg/rule.py | 29 +++++++++++++++++++++++------
2 files changed, 27 insertions(+), 9 deletions(-)
diff --git a/rpg/digest.py b/rpg/digest.py
index 9d8bcf4..ca94621 100644
--- a/rpg/digest.py
+++ b/rpg/digest.py
@@ -243,13 +243,14 @@ def one_digest(pep, enz):
ret.inc_nb_cleavage()
# current position
previous_pos = pos
- # Default: do not cut this position
- cut = False
before = True
# Check each rules
for rul in enz.rules:
+ # Default: do not cut this position
+ cut = None
# Apply the rule: if we need to cut
- if rule.handle_rule(pep.sequence, pos, rul, cut):
+ cut = rule.handle_rule(pep.sequence, pos, rul, cut)
+ if cut is True:
# Random to handle miscleavage
tmp_rand = random.random() * 100
# Rand > ratio_miscleavage, no miscleavage occurs
diff --git a/rpg/rule.py b/rpg/rule.py
index 8c1312d..6dcf802 100644
--- a/rpg/rule.py
+++ b/rpg/rule.py
@@ -786,7 +786,7 @@ def handle_rule(seq, pos, a_rule, cut):
:type cut: bool
:return: `True` if sequence must be cutted
- :rtype: bool
+ :rtype: bool or None
"""
# return of the function: should we cut this?
@@ -799,11 +799,28 @@ def handle_rule(seq, pos, a_rule, cut):
# If the rule applies, i.e. the letter to watch is the good one
if (pos + a_rule.index) >= 0 and \
seq[pos + a_rule.index] == a_rule.letter:
- ret = a_rule.cut
- # Handle the rules (exceptions)
- for rul in a_rule.rules:
- # Apply the rule: do we need to cut?
- ret = handle_rule(seq, pos, rul, ret)
+ # If no previous 'False' and this is cutting
+ if a_rule.cut and ret is not False:
+ ret = True
+ # Handle the sub-rules (exceptions)
+ for rul in a_rule.rules:
+ # Apply the rule: do we need to cut?
+ ret = handle_rule(seq, pos, rul, ret)
+ # Is is not cutting
+ elif not a_rule.cut:
+ # Reinit
+ ret = None
+ # Handle sub-rules
+ if a_rule.rules:
+ # Handle the rules (exceptions)
+ for rul in a_rule.rules:
+ # Apply the rule: do we need to cut?
+ ret = handle_rule(seq, pos, rul, ret)
+ # No sub-rules and not cutting
+ else:
+ # We are at the end a of rule that applies
+ # and say to NOT cut. So it will never cut.
+ ret = False
# Doesn't work: begin or end of sequence, don't change cut value
except IndexError:
pass
--
GitLab