#!/usr/bin/env python ############################################################################ # Copyright (c) 2015-2016 Saint Petersburg State University # Copyright (c) 2011-2015 Saint Petersburg Academic University # All Rights Reserved # See file LICENSE for details. ############################################################################ import sys import os import shutil from quast_libs import qconfig qconfig.check_python_version() from quast_libs.metautils import Assembly, correct_meta_references, correct_assemblies, \ get_downloaded_refs_with_alignments, partition_contigs, calculate_ave_read_support from quast_libs.options_parser import parse_options, remove_from_quast_py_args from quast_libs import contigs_analyzer, reads_analyzer, search_references_meta from quast_libs import qutils from quast_libs.qutils import cleanup, check_dirpath from quast_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'))
############################################################################ # Copyright (c) 2015-2017 Saint Petersburg State University # Copyright (c) 2011-2015 Saint Petersburg Academic University # All Rights Reserved # See file LICENSE for details. ############################################################################ from __future__ import with_statement from __future__ import division import os from collections import defaultdict from quast_libs import qconfig qconfig.check_python_version() from quast_libs import contigs_analyzer, fastaparser, reporting, plotter_data from quast_libs import qutils from quast_libs.qutils import correct_seq, correct_name, get_uniq_name, is_python2 from quast_libs.log import get_logger logger = get_logger(qconfig.LOGGER_META_NAME) class Assembly: def __init__(self, fpath, label): self.fpath = fpath self.label = label self.name = os.path.splitext(os.path.basename(self.fpath))[0] def parallel_partition_contigs(asm, assemblies_by_ref, corrected_dirpath, alignments_fpath_template): assembly_label = qutils.label_from_fpath(asm.fpath)