# Copyright (c) 2011-2015 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
from __future__ import with_statement
import sys
import os
import shutil
from libs import qconfig
from libs.metautils import remove_from_quast_py_args, Assembly, correct_meta_references, correct_assemblies, \
get_downloaded_refs_with_alignments, partition_contigs
from libs.options_parser import parse_options
qconfig.check_python_version()
from libs import contigs_analyzer, reads_analyzer, search_references_meta
from libs import qutils
from libs.qutils import cleanup
from libs.log import get_logger
logger = get_logger(qconfig.LOGGER_META_NAME)
logger.set_up_console_handler()
from site import addsitedir
addsitedir(os.path.join(qconfig.LIBS_LOCATION, 'site_packages'))
def _start_quast_main(args,
assemblies,
reference_fpath=None,
############################################################################
# Copyright (c) 2011-2014 Saint-Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import sys
import os
import shutil
import getopt
quast_dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
sys.path.append(os.path.join(quast_dirpath, 'libs'))
from libs import qconfig
qconfig.check_python_version()
from libs import qutils, fastaparser
from libs.qutils import assert_file_exists
from libs.log import get_logger
logger = get_logger('metaquast')
logger.set_up_console_handler()
from site import addsitedir
addsitedir(os.path.join(quast_dirpath, 'libs', 'site_packages'))
import quast
COMBINED_REF_FNAME = 'combined_reference.fasta'