# Path: abstar/core/germline.py
# def get_germline_database_directory(species, receptor='bcr'):
#     species = species.lower()
#     receptor = receptor.lower()
#     addon_dir = os.path.expanduser(f'~/.abstar/germline_dbs/{receptor}')
#     if os.path.isdir(addon_dir):
#         if species.lower() in [os.path.basename(d[0]) for d in os.walk(addon_dir)]:
#             return os.path.join(addon_dir, species.lower())
#     mod_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
#     return os.path.join(mod_dir, f'assigners/germline_dbs/{receptor}/{species}')


import logging
import os
import traceback
from Bio import SeqIO
from Bio.Seq import Seq
from abutils.core.sequence import Sequence
from abutils.utils import log
from abutils.utils.alignment import local_alignment
from abutils.utils.decorators import lazy_property
from ..core.germline import get_germline_database_directory
#
# Copyright (c) 2015 Bryan Briney
# License: The MIT license (http://opensource.org/licenses/MIT)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge, publish, distribute,
# sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all copies or
# substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
# BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#


from __future__ import absolute_import, division, print_function, unicode_literals






def get_isotype(antibody):
    try:

# Path: abstar/core/germline.py
# def get_germline_database_directory(species, receptor='bcr'):
#     species = species.lower()
#     receptor = receptor.lower()
#     addon_dir = os.path.expanduser(f'~/.abstar/germline_dbs/{receptor}')
#     if os.path.isdir(addon_dir):
#         if species.lower() in [os.path.basename(d[0]) for d in os.walk(addon_dir)]:
#             return os.path.join(addon_dir, species.lower())
#     mod_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
#     return os.path.join(mod_dir, f'assigners/germline_dbs/{receptor}/{species}')


# Path: abstar/utils/isotype.py
import logging
import os
import traceback
from Bio import SeqIO
from Bio.Seq import Seq
from abutils.core.sequence import Sequence
from abutils.utils import log
from abutils.utils.alignment import local_alignment
from abutils.utils.decorators import lazy_property
from ..core.germline import get_germline_database_directory

#
# Copyright (c) 2015 Bryan Briney
# License: The MIT license (http://opensource.org/licenses/MIT)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge, publish, distribute,
# sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all copies or
# substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
# BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#


from __future__ import absolute_import, division, print_function, unicode_literals






def get_isotype(antibody):
    try:

        germ_dir = get_germline_database_directory(antibody.germ_db)