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)