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,