from general import UtilsPipeline
from general import UtilsTools
from general import UtilsAlignment
from general import UtilsAnnotations
from objects import SortedExonsAttributes
from metrics import TranscriptsMetrics
from metrics import GeneDatabaseMetrics
from metrics import ReadsCoverage
from report import ShortReport
from report import SeparatedReport
from report import ComparisonReport
logger = log.get_logger(rqconfig.LOGGER_DEFAULT_NAME)
from general.rqconfig import PRECISION
def main_utils():
program_name = sys.argv[0][:sys.argv[0].rfind('.')]
# parse running string of main program and get all arguments:
args = UtilsPipeline.get_arguments()
WELL_FULLY_COVERAGE_THRESHOLDS = rqconfig.well_fully_coverage_thresholds(
args.lower_threshold, args.upper_threshold)
ALIGNMENT_THRESHOLDS = rqconfig.alignment_thresholds()
this_location = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
sys.path.append(os.path.join(this_location, 'quast_libs'))
from quast_libs import qutils
from quast_libs import fastaparser
if qutils.is_python2():
from quast_libs.site_packages.joblib2 import Parallel, delayed
else:
from quast_libs.site_packages.joblib3 import Parallel, delayed
from general import log
from general import rqconfig
logger = log.get_logger('parallel_blat_run')
def parallel_blat_run(transcripts_dict, reference_pathes, threads, tmp_dir,
label, logger, log_dir):
log_out_1 = os.path.join(log_dir, label + '.blat.out.log')
logger.print_timestamp()
logger.info('Getting psl files by BLAT for {}...'.format(label))
output_dirs = []
tmp_dirs = []
us_threads = min(threads, len(transcripts_dict))
# CREATE TEMPORARY DIRECTORIES FOR THREADS: