From 1d0dbc36a389454483e20beb5e575e25b2556d6a Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 2 Dec 2011 13:59:31 +0000
Subject: [PATCH] Fixed a bug in genbank.py that was triggered while building a
list of tags from the product list. Please check this fix.
Made some trivial changes in the rest of the files.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@431 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
INSTALL | 2 +-
extras/post-install.sh | 1 +
mutalyzer/Crossmap.py | 2 ++
mutalyzer/parsers/genbank.py | 15 ++++++++-------
4 files changed, 12 insertions(+), 8 deletions(-)
diff --git a/INSTALL b/INSTALL
index 511ed443..fe72b616 100644
--- a/INSTALL
+++ b/INSTALL
@@ -39,7 +39,7 @@ Short version
Run the following commands:
- svn https://www.mutalyzer.nl/svn/mutalyzer2/trunk .
+ svn co https://www.mutalyzer.nl/svn/mutalyzer2/trunk .
sudo bash extras/pre-install.sh
sudo python setup.py install
sudo bash extras/post-install.sh
diff --git a/extras/post-install.sh b/extras/post-install.sh
index 0f5a249a..57043eb3 100644
--- a/extras/post-install.sh
+++ b/extras/post-install.sh
@@ -46,6 +46,7 @@ for USERNAME in $(cut -f 1 -d : /etc/passwd); do
if [ -d "/home/${USERNAME}" ]; then
echo -e "${COLOR_INFO}Creating /home/${USERNAME}/.config/mutalyzer/config${COLOR_END}"
echo -e "${COLOR_INFO}Creating /home/${USERNAME}/.cache/mutalyzer${COLOR_END}"
+ # Instead of su, use chown later.
su $USERNAME -c "mkdir -p /home/$USERNAME/.config/mutalyzer"
su $USERNAME -c "mkdir -p /home/$USERNAME/.cache/mutalyzer"
su $USERNAME -c "touch /home/$USERNAME/.config/mutalyzer/config"
diff --git a/mutalyzer/Crossmap.py b/mutalyzer/Crossmap.py
index 20fb8edc..38509187 100644
--- a/mutalyzer/Crossmap.py
+++ b/mutalyzer/Crossmap.py
@@ -564,6 +564,7 @@ class Crossmap() :
"""
return len(self.RNA) / 2 - 1
+ #numberOfIntrons
def numberOfExons(self) :
"""
@@ -574,6 +575,7 @@ class Crossmap() :
"""
return len(self.RNA) / 2
+ #numberOfExons
#Crossmap
#
diff --git a/mutalyzer/parsers/genbank.py b/mutalyzer/parsers/genbank.py
index 2b3b94df..69e3fd3d 100644
--- a/mutalyzer/parsers/genbank.py
+++ b/mutalyzer/parsers/genbank.py
@@ -181,13 +181,14 @@ class GBparser():
i = 0
while i < productList[0].count(' ') + 1 :
for j in range(1, len(productList)) :
- if productList[0][::direction].split(' ')[i] != \
- productList[j][::direction].split(' ')[i] :
- if direction == 1 :
- return i
- else :
- return productList[0].count(' ') - i + 1
- #if
+ if i <= productList[j].count(' ') :
+ if productList[0][::direction].split(' ')[i] != \
+ productList[j][::direction].split(' ')[i] :
+ if direction == 1 :
+ return i
+ else :
+ return productList[0].count(' ') - i + 1
+ #if
i += 1
#while
return 0
--
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