def build_pmt_seq_data(bp_size=None):
# Insert into database
dbManager = dbm.DBManagerPG(settings.conn_string)
if bp_size is None:
dbManager.import_pmt_seq_data()
elif bp_size == '1k':
dbManager.import_pmt_seq_data(seq_type='m1', pmt_fasta_file_path=settings.seq_pmt_1k)
elif bp_size == '5k':
dbManager.import_pmt_seq_data(seq_type='m5', pmt_fasta_file_path=settings.seq_pmt_5k)
def build_walley_data():
# Read data from csv and build data set into list
fm = fManager.FileManager()
ld_prot = fm.csv2list(settings.walley_prot)
ld_gene = fm.csv2list(settings.walley_gene)
print (len(ld_prot), len(ld_prot[0]))
print (len(ld_gene), len(ld_gene[0]))
# Insert into database
dbManager = dbm.DBManagerPG(settings.conn_string)
dbManager.build_walley_data(ld_prot, 'p')
dbManager.build_walley_data(ld_gene, 'g')
def build_kmers():
""" Build kmers dataset for pepide sequence
Args:
None
Return:
None
"""
dbManager = dbm.DBManagerPG(settings.conn_string)
dbManager.build_kmers(3)
dbManager.build_kmers(2)
def build_kmers(is_promoter=False, bp_size=None):
dbManager = dbm.DBManagerPG(settings.conn_string)
if is_promoter:
for k in range(7, 0, -1):
print('{}-mer creating...'.format(k))
if bp_size is None or bp_size == '1k':
dbManager.build_promoter_kmers(k=k)
elif bp_size == '5k':
dbManager.build_promoter_kmers(k=k, bp_size='5k')
else:
dbManager.build_promoter_kmers(k=k)
else:
#dbManager.build_kmers(3)
#dbManager.build_kmers(2)
dbManager.build_kmers(1)
def build_dna_seq_data():
# Insert into database
dbManager = dbm.DBManagerPG(settings.conn_string)
dbManager.import_dna_seq_data()
def build_kmers_pm():
dbManager = dbm.DBManagerPG(settings.conn_string)
dbManager.build_kmers(3)
from flask import Flask, request, render_template, session, redirect
from utils import DBManager
from datetime import datetime
app = Flask(__name__)
app.secret_key = "rexrexrex"
dbm = DBManager('root', '')
def get_current_sem():
now = datetime.now()
if now.month >= 6:
semester = 'Fall {}'.format(now.year)
else:
semester = 'Spring {}'.format(now.year)
return semester
def get_next_sem():
now = datetime.now()
if now.month >= 6:
semester = 'Spring {}'.format(now.year + 1)
else:
semester = 'Fall {}'.format(now.year)
return semester
@app.route("/")
@app.route("/home")
def home():
if 'access' in session:
def get_sample_code():
dbManager = dbm.DBManagerPG(settings.conn_string)
sample_code = dbManager.get_sample_code()
return sample_code
def build_ra_mapping_table():
dbManager = dbm.DBManagerPG(settings.conn_string)
dbManager.build_ra_mapping_table()