PartsDB

SQLAlchemy extension for registries of biological parts

Installation

The easiest way to install is by using pip:

pip install .

Example

PartsDB assumes you already have some DB server installed. If you don't have one, try PostgreSQL.

Once installed, create a new database. In Linux or MacOS, this can be done by:

createdb [dbname]

Then you need to define some tables for your database. The system/Tables.py file has some useful MixIns which can be used to define tables for your database. For example:

class Promoter(Base,BaseMixIn,PartMixIn):
	pass

class CDS(Base,BaseMixIn,PartMixIn):
	pass

class Terminator(Base,BaseMixIn,PartMixIn):
	pass

class Gene(Base,BaseMixIn):
	name 			= Column( String(100) )
	promoterID  	= Column( Integer, ForeignKey('promoter.id') )
	cdsID  			= Column( Integer, ForeignKey('cds.id') )
	terminatorID  	= Column( Integer, ForeignKey('terminator.id') )

	promoter 		= relationship(Promoter, 	enable_typechecks=False)
	cds 			= relationship(CDS, 		enable_typechecks=False)
	terminator 		= relationship(Terminator, 	enable_typechecks=False)

defines three tables for parts (uses PartMixIn): Promoter, CDS, Terminator; and a Gene table (only uses BaseMixIn), which is a particular combination of one of each.

Then, communication with your database is easy as:

• Importing PartsDB and your table definitions

from partsdb.partsdb import PartsDB
from tables import *

• Creating a connection to your database

partsdb = PartsDB('postgresql:///dbname', clean = True, Base = Base)

Where dbname is a name of the database you have created. The clean = True flag erases all rows in all entries.

• Adding some parts

promoter 	= partsdb.addPart('promoter', seq = "TTACGTA")
cds		 	= partsdb.addPart('cds', seq = "ATGTAA")
terminator 	= partsdb.addPart('terminator', seq = "GCGCGTA")

gene = partsdb.addPart('gene', promoter = promoter, cds = cds, terminator = terminator)

partsdb.commit()

Note, that the seq column is defined in PartsMixIn in system/Tables.py. The commit() is essential for new records to be added to the databse.

• Querying the databse

session = partsdb.Session()
query = session.query(Gene).first()
session.close()

• Accessing record information

print query.dbid
print query.promoter.seq + query.cds.seq + query.terminator.seq

Have a try with files in the example folder.