def main():
# Create up the database session
dbi = DatabaseInterface(can_email = True)
tsession = dbi.get_session()
# Create a map from usernames to the database IDs (typically initials)
user_map = {}
for u in tsession.query(Users):
user_map[u.lab_username] = u.ID
# Read the import path from the database
colortext.message('\nPrimers import script')
colortext.pcyan('Database admin contacts: {0}'.format(', '.join(dbi.get_admin_contacts())))
colortext.warning('Registered users: {0}\n'.format(', '.join( ['{0} ({1})'.format(v, k) for k, v in sorted(user_map.iteritems(), key = lambda x: x[1])])))
errors = []
import_path = tsession.query(DBConstants).filter(DBConstants.Parameter == u'import_path').one().Value
import_path_folders = sorted([d for d in os.listdir(import_path) if os.path.isdir(os.path.join(import_path,d))])
for ipf in import_path_folders:
if ipf in user_map:
user_folder = os.path.join(import_path, ipf)
user_id = user_map[ipf]
primers_file = os.path.join(user_folder, 'primers.tsv')
if os.path.exists(primers_file):
case_errors = []
try:
parse(dbi, primers_file, user_id, case_errors)
if case_errors:
errors.append("Errors occurred processing '{0}':\n\t{1}".format(primers_file, '\n\t'.join(case_errors)))
colortext.warning(errors[-1])
except Exception, e:
errors.append("Errors occurred processing '{0}': {1}\n\t{2}\n{3}".format(primers_file, str(e), '\n\t'.join(case_errors), traceback.format_exc()))
colortext.warning('Error: {0}\n{1}'.format(str(e), traceback.format_exc()))
#!/usr/bin/python
# encoding: utf-8
"""
ligand.py test code.
Created by Shane O'Connor 2016
"""
import sys
import os
sys.path.insert(0, os.path.join('..', '..'))
from klab.bio.ligand import Ligand, PDBLigand
from klab import colortext
l = Ligand.retrieve_data_from_rcsb('NAG', pdb_id = '1WCO', silent = True, cached_dir = '/tmp')
colortext.warning(l)
l = Ligand.retrieve_data_from_rcsb('GDP', silent = True, cached_dir = '/tmp')
colortext.pcyan(l)
l = PDBLigand.instantiate_from_ligand(l, 'A', ' 124B')
colortext.porange(l)
l = PDBLigand.retrieve_data_from_rcsb('GOL', '1BXO', 'A', ' 12B', pdb_ligand_code='TST', silent = True, cached_dir = '/tmp')
colortext.ppurple(l)
c += 1
colortext.message('\n{0}/{1}: {2}'.format(c, len(pdb_ids), pdb_id))
hits = b.by_pdb(pdb_id)
if hits:
colortext.warning('{0} hits: {1}'.format(len(hits), ','.join(hits)))
else:
colortext.warning('No hits')
except Exception, e:
colortext.error('FAILED')
failed_cases.append((pdb_id, str(e), traceback.format_exc()))
if failed_cases:
colortext.warning('*** These cases failed ***')
for p in failed_cases:
print('')
colortext.pcyan(p[0])
colortext.error(p[1])
print(p[2])
print('')
def test_sequences(b, sequences):
failed_cases = []
c = 0
for sequence in sequences:
try:
c += 1
colortext.message('\n{0}/{1}: {2}'.format(c, len(sequences), sequence))
hits = b.by_sequence(sequence)
if hits:
colortext.warning('{0} hits: {1}'.format(len(hits), ','.join(hits)))
