def query(r, d, query_sdf, ref_iddb, embedOnly=False):
current_dir = os.path.abspath(".")
query_sdf = os.path.join(current_dir, query_sdf)
ref_iddb = os.path.join(current_dir, ref_iddb)
work_dir = os.path.join(current_dir, 'run-%s-%s' % (r, d))
if not os.path.isfile(query_sdf):
raise StandardError("query file " + query_sdf + " not found")
if not os.path.isfile(ref_iddb):
raise StandardError("reference file " + ref_iddb + " not found")
if not os.path.isdir(work_dir):
raise StandardError("working directory " + work_dir + " not found")
temp_dir = mkdtemp()
query_base = os.path.splitext(os.path.basename(query_sdf))[0]
query_cdb = os.path.join(temp_dir, query_base + ".cdb")
matrix_file = os.path.join(work_dir, "matrix.%s-%s" % (r, d))
coord_file = ref_iddb + ".distmat.coord"
try:
#TODO move this to non-batch branch and check
parsing_time, num_compounds = createQueryCdb(query_sdf, query_cdb)
info("found %s compounds" % num_compounds)
ref_db = gen_subdb(ref_iddb, None, DB_SUBSET, CDB)
names = [i.strip() for i in file(CDB + ".names")]
f = file(query_base + ".out", 'w')
os.chdir(temp_dir)
if embedOnly or num_compounds > 1:
batchQuery(f, r, d, ref_db, query_sdf, coord_file, matrix_file,
names, embedOnly)
else:
puzzle_file = os.path.join(temp_dir, "puzzle")
refineResult = refine(
QueryFile(query_cdb),
lshSearch(
matrix_file,
solvePuzzle(r, d, ref_db, query_cdb, coord_file,
puzzle_file)))
for seq_id, dist in refineResult:
f.write('%s %s\n' % (names[int(seq_id) - 1], dist))
info("refine result: " + str(refineResult))
f.close()
os.chdir(current_dir)
from shutil import rmtree
#warning("NOT CLEANING UP")
rmtree(temp_dir)
except:
print_exc()
def query(r,d,query_sdf,ref_iddb,embedOnly=False):
current_dir = os.path.abspath(".")
query_sdf = os.path.join(current_dir,query_sdf)
ref_iddb = os.path.join(current_dir,ref_iddb)
work_dir = os.path.join(current_dir,'run-%s-%s' % (r, d))
if not os.path.isfile(query_sdf):
raise StandardError("query file "+query_sdf+" not found")
if not os.path.isfile(ref_iddb):
raise StandardError("reference file "+ref_iddb+" not found")
if not os.path.isdir(work_dir):
raise StandardError("working directory "+work_dir+" not found")
temp_dir=mkdtemp()
query_base = os.path.splitext(os.path.basename(query_sdf))[0]
query_cdb = os.path.join(temp_dir,query_base+".cdb")
matrix_file = os.path.join(work_dir,"matrix.%s-%s" % (r,d))
coord_file = ref_iddb+".distmat.coord"
try:
#TODO move this to non-batch branch and check
parsing_time,num_compounds = createQueryCdb(query_sdf,query_cdb)
info("found %s compounds" % num_compounds)
ref_db = gen_subdb(ref_iddb,None,DB_SUBSET,CDB)
names = [i.strip() for i in file(CDB+".names")]
f = file(query_base+".out",'w')
os.chdir(temp_dir)
if embedOnly or num_compounds > 1:
batchQuery(f,r,d,ref_db,query_sdf,
coord_file,matrix_file,names,embedOnly)
else:
puzzle_file = os.path.join(temp_dir,"puzzle")
refineResult = refine(QueryFile(query_cdb),
lshSearch(matrix_file,
solvePuzzle(r,d,ref_db,query_cdb,
coord_file,puzzle_file)))
for seq_id,dist in refineResult:
f.write('%s %s\n' %(names[int(seq_id)-1],dist))
info("refine result: "+str(refineResult))
f.close()
os.chdir(current_dir)
from shutil import rmtree
#warning("NOT CLEANING UP")
rmtree(temp_dir)
except:
print_exc()
sys.stderr.write("Invalid reference coordinate file: no such file.")
sys.stderr.write("Missing:\n")
sys.stderr.write(ref_coord)
sys.exit(1)
f = file(ref_coord)
d = len(f.readline().split())
for i, _ in enumerate(f): pass
r = 2 + i
sys.stderr.write("r = %d d = %d\n" % (r, d))
db_builder = DB_BUILDER
db2db_distance = DB2DB_DISTANCE
if opts.m:
db_builder += ('.' + opts.m)
db2db_distance += ('.' + opts.m)
# this assumes absolute paths, which we don't need to have
#if not os.path.isfile(db_builder):
#sys.stderr.write("Cannot find database builder to parse your input")
#sys.stderr.write("\nI cannot find: ")
#sys.stderr.write(db_builder)
#sys.exit(1)
ref_real_db = gen_subdb(ref_db_path, opts.m,DB_SUBSET,CDB)
print embed(args[0], r, d, ref_real_db, ref_coord, db_builder, db2db_distance)
# vim:tw=78:ts=4:sw=4:expandtab
sys.stderr.write(ref_coord)
sys.exit(1)
f = file(ref_coord)
d = len(f.readline().split())
for i, _ in enumerate(f):
pass
r = 2 + i
sys.stderr.write("r = %d d = %d\n" % (r, d))
db_builder = DB_BUILDER
db2db_distance = DB2DB_DISTANCE
if opts.m:
db_builder += ('.' + opts.m)
db2db_distance += ('.' + opts.m)
# this assumes absolute paths, which we don't need to have
#if not os.path.isfile(db_builder):
#sys.stderr.write("Cannot find database builder to parse your input")
#sys.stderr.write("\nI cannot find: ")
#sys.stderr.write(db_builder)
#sys.exit(1)
ref_real_db = gen_subdb(ref_db_path, opts.m, DB_SUBSET, CDB)
print embed(args[0], r, d, ref_real_db, ref_coord, db_builder,
db2db_distance)
# vim:tw=78:ts=4:sw=4:expandtab
