diff --git a/INSTALL b/INSTALL index 511ed443201ad7ebdb8f8011bcddee06e58c31ec..fe72b61625073c44d66ed1aa91bfff68513fe557 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 0f5a249af46d2796f3af1b3db7a02571c2f14d53..57043eb38545d01d5114aa5c80a5ac1f0d94d8c4 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 20fb8edc6147cb09c289a7754ab8dd2180b6ca1b..3850918745f92363ca3c97f92786b596429ce438 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 2b3b94df8b1c77936fba2138cf38cf4c815c0594..69e3fd3d21e832ec4d912f55f6193bfdb4fa0d04 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