Commit 2f0f6f01 authored by Mathieu Courcelles's avatar Mathieu Courcelles

Fixes K-K filter bug (Issue #31)

parent 44a8598a
Pipeline #32004072 passed with stages
## Copyright 2013-2017 Mathieu Courcelles
## Copyright 2013-2018 Mathieu Courcelles
## Mike Tyers's lab / IRIC / Universite de Montreal
# Import standard librariesdjang
# Import standard libraries
import subprocess
import os
import tempfile
......@@ -167,6 +167,9 @@ class DatasetProcessing:
#print instance.clpeptidefilter.KK_link
if instance.clpeptidefilter.KK_link:
if not clpep.cross_link:
continue
if clpep.pep1_link_pos == 1:
continue
......@@ -183,8 +186,12 @@ class DatasetProcessing:
if aa1 != 'K':
continue
aa2 = clpep.peptide_wo_mod2[clpep.pep2_link_pos - 1]
if clpep.link_type == 'Intra-peptide':
aa2 = clpep.peptide_wo_mod1[clpep.pep2_link_pos - 1]
else:
aa2 = clpep.peptide_wo_mod2[clpep.pep2_link_pos - 1]
#print ('%s-%s') % (aa1, aa2)
#print aa1 != aa2
......
......@@ -16,13 +16,13 @@ Notes:
-Python should be already installed. If not type the following command to install it:
sudo apt-get install python
sudo apt-get install python-pip
sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose libmysqlclient-dev
3. Navigate to the CLMSVault directory by typing:
cd /home/user/CLMSVault
4. Install the remaining Python libraries by typing:
pip install -r requirements/production.txt
pip install -r requirements/base.txt
5. Add environment variables
nano ~/.profile
......@@ -41,7 +41,7 @@ chmod +x CLMSVault_linux.sh
./CLMSVault/settings/local.py (ADMINS, TIME_ZONE)
8. Start the application web server from the console:
./CLMSVault_win.sh
./CLMSVault.sh
9. Use your web browser to access CLMSVault at: http://localhost:8000
......
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