Providing generating database class and query/filter DB interfaces for running simulation model
sudo apt-get install libsqlite3-dev
pip install --install-option="--prefix=${PREFIX}" -r requeirements.txt # if non-root user
python setup.py install --prefix=${PREFIX}
Install virtualenv
pip install viratualenv virtualenvwrapper
Added the following in .zshrc or .bashrc
export WORKON_HOME=$HOME/.virtualenvs
if [ -f path_to_your_env/bin/virtualenvwrapper.sh ]; then
source path_to_your_env/bin/virtualenvwrapper.sh
fiInto virtualenv and add ${PYTHONPATH} to this project directory
mkvirtualenv ecellp
workon ecellp
add2virtualenv "/home/soh.i/E-cell_Sprint/ecellp/src"
python setup.py testSample code is query_test.py in samples directory.
PYTHONPATH=${PREFIX}/lib/python2.7/site-packages #not necessary for virtualenv
python samples/query_test.py
Add relative path from APP_ROOT to your data files.
[input_data]
sequence=/data/test.fafrom ecellp import session
db_config = session.DBConfig()
# pass absolute path to your conf.ini
# db_config = session.DBConfig(file=os.path.abspath('./conf.ini'))
# pass a dict containing paths to your data
# db_config = session.DBConfig(paths={'sequence':'/data/test.fa'})
query = session.QueryBuilder(db_config)
print query.count_stored_records()
#=> 4145
print query.collect_cds_records()
#=> return All CDS annotations ans its sequences
print query.find_by_name('thrL')
#=> <Species('thrL','1','189','255','CDS','ATGAAACGCATTACCACCACCAT...')>
print query.collect_annotations_filter_by_strand(-1)
#=> return annotations and sequence on complement strand
print query.include_gene_in_region(21, 2012)
#=> [u'thrL', u'thrA']
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