import sys
from partsdb.partsdb import PartsDB
from partsdb.tools.Populators import PlantPopulator
from .tables import *
from partsdb.tools.Exporters import GenBankExporter
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from Bio.SeqFeature import SeqFeature
genomeFileName = 'data/mapped/genome.fa'
transcriptFileName = 'data/mapped/trans.fa'
proteinFileName = 'data/mapped/pep.fa'
mapFileName = 'data/mapped/map.gff3'
marpodb = PartsDB('postgresql:///'+sys.argv[1], clean = True, Base = Base)
marpodb.setup(prefix = "mpdb")
ppl = PlantPopulator(marpodb)
ppl.populate(mapFileName, transcriptFileName, proteinFileName, genomeFileName)
import sys
from partsdb.partsdb import PartsDB
from tables import *
marpodb = PartsDB('postgresql:///' + sys.argv[1], Base=Base)
session = marpodb.Session()
n = 0
i = 0
for gene in session.query(Gene).all():
nHits = session.query(
InterProHit.id).filter(InterProHit.targetID == gene.cds.id).count()
if nHits == 0:
session.query(BlastpHit).filter(
BlastpHit.targetID == gene.cds.id).delete()
session.query(DbxRef).filter(DbxRef.targetID == gene.cds.id).delete()
session.delete(gene.cds)
if gene.utr5:
session.delete(gene.utr5)
if gene.utr3:
session.delete(gene.utr3)
session.delete(gene)
n = n + 1
if i % 10 == 0:
print "Processed {0} genes, deleted {1}".format(i, n)
i = i + 1
from partsdb.partsdb import PartsDB
from tables import *
partsdb = PartsDB('postgresql:///partsdb', clean = True, Base = Base)
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()
session = partsdb.Session()
query = session.query(Gene).first()
session.close()
print query.dbid
print query.promoter.seq + query.cds.seq + query.terminator.seq
import sys
from partsdb.partsdb import PartsDB
from tables import *
marpodb = PartsDB('postgresql:///'+sys.argv[1], Base = Base)
marpodb.annotate('blastphit', fileName = 'data/filtered/blastp.info')
marpodb.annotate('interprohit', fileName = 'data/interpro.list')
marpodb.annotate('dbxref', fileName = 'data/DbxRef.list')
import sys
from partsdb.partsdb import PartsDB
from .tables import *
marpodb = PartsDB('postgresql:///' + sys.argv[1], Base=Base)
marpodb.annotate('blastphit', fileName='data/filtered/blastp.info')
marpodb.annotate('pfamhit', fileName='data/filtered/Pfam.domtblout')
from flask_user import UserMixin, SQLAlchemyAdapter, UserManager, LoginManager
from flask_login import login_user, login_required, logout_user, current_user, user_logged_in
from .user import RegisterForm, LoginForm
from .system import getUserData, generateNewMap, getTopGenes, processQuery, getGeneCoordinates, getCDSDetails, parseBlastResult, recfind
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from Bio.Alphabet import IUPAC
import os
import sys
import subprocess
marpodb = PartsDB('postgresql:///' + os.environ["MARPODB_DB_NAME"], Base=Base)
app = Flask(__name__)
app.secret_key = 'HJKDGSA&^D%HJKN.zczxcoasdk2194uru'
app.config['SQLALCHEMY_DATABASE_URI'] = "postgresql:///userdb"
app.debug = True
userDB = SQLAlchemy(app)
loginManager = LoginManager()
loginManager.init_app(app)
class User(userDB.Model, UserMixin):
id = userDB.Column(userDB.Integer(), primary_key=True)
username = userDB.Column(userDB.String(50), nullable=False, unique=True)
password = userDB.Column(userDB.String(500),
from partsdb.partsdb import PartsDB
from tables import *
import os
from partsdb.tools.Exporters import GenBankExporter
if "MARPODB_DB_NAME" in os.environ:
dbName = '/' + os.environ["MARPODB_DB_NAME"]
else:
dbName = "marpodb.io/marpodb3?user=common"
marpodb = PartsDB('postgresql://' + dbName, Base=Base)
session = marpodb.Session()
exporter = GenBankExporter(None)