def get_sifts_object(self, pdb_id, acceptable_sequence_percentage_match = 90.0, restrict_match_percentage_errors_to_these_uniparc_ids = None):
# todo: we need to store all/important parameters for object creation and key on those as well e.g. "give me the SIFTS object with , restrict_match_percentage_errors_to_these_uniparc_ids = <some_set>"
# otherwise, unexpected behavior may occur
self.log_lookup('SIFTS object {0}'.format(pdb_id))
pdb_id = pdb_id.upper()
if not self.sifts_objects.get(pdb_id):
if not self.sifts_xml_contents.get(pdb_id):
if self.cache_dir:
self.add_sifts_xml_contents(pdb_id, download_sifts_xml(pdb_id, self.cache_dir, silent = True))
else:
self.add_sifts_xml_contents(pdb_id, retrieve_sifts_xml(pdb_id, silent = True))
self.add_sifts_object(pdb_id, SIFTS.retrieve(pdb_id, cache_dir = self.cache_dir, acceptable_sequence_percentage_match = acceptable_sequence_percentage_match, bio_cache = self, restrict_match_percentage_errors_to_these_uniparc_ids = restrict_match_percentage_errors_to_these_uniparc_ids))
return self.sifts_objects[pdb_id]
#!/usr/bin/python
# encoding: utf-8
"""
sifts.py test code.
Created by Shane O'Connor 2016
"""
import sys
import os
import time
import pprint
sys.path.insert(0, os.path.join('..', '..'))
from klab import colortext
from klab.bio.sifts import SIFTS
#for pdb_id in ['1AQT', '1lmb', '1utx', '2gzu', '2pnr', '1y8p', '2q8i', '1y8n', '1y8o', '1oax', '3dvn', '1mnu', '1mcl', '2p4a', '1s78', '1i8k']:
for pdb_id in ['2pnr']:
print('\n')
colortext.message(pdb_id)
s = SIFTS.retrieve(pdb_id, cache_dir = '/kortemmelab/data/oconchus/SIFTS', acceptable_sequence_percentage_match = 70.0)
colortext.warning(pprint.pformat(s.region_mapping))
colortext.warning(pprint.pformat(s.region_map_coordinate_systems))
colortext.warning(pprint.pformat(s.pfam_scop_mapping))
colortext.warning(pprint.pformat(s.scop_pfam_mapping))
print('\n')
print('\n\n')