# Path: crumbs/utils/optional_modules.py
# MSG = 'A python package to run this executable is required,'
# BIO = 'biopython'
# BIO_BGZF = 'biopython with Bgzf support'
#     NCBIXML = create_fake_class(MSG + BIO)
#     NCBIWWW = create_fake_class(MSG + BIO)
# def create_fake_class(msg):
#         def __init__(self, *args, **kwargs):
# def create_fake_funct(msg):
#     def FakeRequiredfunct(*args, **kwargs):
#     class FakePythonRequiredClass(object):


from array import array
from crumbs.utils.optional_modules import SffIterator
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of seq_crumbs.
# seq_crumbs is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.

# seq_crumbs is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR  PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with seq_crumbs. If not, see <http://www.gnu.org/licenses/>.

from __future__ import division


# pylint: disable=R0913


def _min_left_clipped_seqs(sff_fhand, trim, min_left_clip):
    'It generates sequences (as tuples) given a path to a SFF file.'

# Path: crumbs/utils/optional_modules.py
# MSG = 'A python package to run this executable is required,'
# BIO = 'biopython'
# BIO_BGZF = 'biopython with Bgzf support'
#     NCBIXML = create_fake_class(MSG + BIO)
#     NCBIWWW = create_fake_class(MSG + BIO)
# def create_fake_class(msg):
#         def __init__(self, *args, **kwargs):
# def create_fake_funct(msg):
#     def FakeRequiredfunct(*args, **kwargs):
#     class FakePythonRequiredClass(object):


# Path: crumbs/seq/sff_extract.py
from array import array
from crumbs.utils.optional_modules import SffIterator

# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of seq_crumbs.
# seq_crumbs is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.

# seq_crumbs is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR  PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with seq_crumbs. If not, see <http://www.gnu.org/licenses/>.

from __future__ import division


# pylint: disable=R0913


def _min_left_clipped_seqs(sff_fhand, trim, min_left_clip):
    'It generates sequences (as tuples) given a path to a SFF file.'

    for record in SffIterator(sff_fhand, trim=False):