E-Cell4 P: Database project for whole cell simulation in E. coli

Description

Providing generating database class and query/filter DB interfaces for running simulation model

Installation

Install dependencies

pip install -r requeirements.txt

Required data

Some required RegulonDB/refSeq dataset are able to download by misc/required_data_downloader.pl, then put those files into data directory.

• NC_000913.gbk
• PromoterSet.txt
• TerminatorSet.txt

Configuration file

Add absolute project root path into conf.ini.

[root]
APP_ROOT=/Users/yukke/dev/DB4E-Cell-P

Running

Sample code is query_test.py in DB4E-Cell-P/db4ecellp directory.

Query genome sequence and annotations

from db4ecellp import db4ecellp
query = db4ecellp.QueryBuilder('./conf.ini') # PATH TO conf.ini

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']