from kdbom2 import kdbom
from sequence import fasta as F
from sequence import blastNoSQL as B
from sequence import aos as A
import numpy as N
SQLservers = (('kf-db1',3306),)
prrsvDB = kdbom.tryDBconnect('PRRSV',SQLservers)
class Sequence(kdbom.KSqlObject):
_table = prrsvDB.Sequence
def generateFasta(self):
'''generates a fasta file using Sequence_ID as
the title and Sequence as the sequence
'''
rec=F.Record(title=self.Sequence_ID, sequence=self.Sequence)
return rec
def taxa(self):
"""return generator of taxa that I belong to
"""
return Taxon.generator(Sequence.Sequence_ID==self)
fasta=generateFasta
class Candidate(kdbom.KSqlObject):
_table = prrsvDB.Candidate
energyStats=dict(
import os
import os.path
import datetime
from types import *
import utils
from __init__ import *
from fasta import *
from blastNoSQL import *
from kdbom2 import kdbom
blastDB = kdbom.tryDBconnect(db='Blast_Results',
serversPorts='kf-db1',
getTables=False,
fatal=True)
SQL = {'createHspTable':
"""
CREATE TABLE IF NOT EXISTS %s (
`Hsp_ID` bigint unsigned NOT NULL AUTO_INCREMENT,
`Q_Gi` varchar(255) NOT NULL,
`T_Gi` varchar(255) NOT NULL,
`Ident` float unsigned NOT NULL,
`Length` int unsigned NOT NULL,
`Gaps` int unsigned NOT NULL,
`Mismatch` int unsigned NOT NULL,
`Q_Start` int unsigned NOT NULL,
`Q_End` int unsigned NOT NULL,
