def create_meta_report(results_dirpath, json_texts):
html_fpath = os.path.join(results_dirpath, report_fname)
if not os.path.isfile(html_fpath):
init(html_fpath, is_meta=True)
from quast_libs import search_references_meta
taxons_for_krona = search_references_meta.taxons_for_krona
meta_log = get_logger(qconfig.LOGGER_META_NAME)
if taxons_for_krona:
create_krona_charts(taxons_for_krona, meta_log, results_dirpath, json_texts)
# reading html template file
with open(html_fpath) as f_html:
html_text = f_html.read()
keyword = 'totalReport'
html_text = re.sub('{{ ' + keyword + ' }}', '[' + ','.join(json_texts) + ']', html_text)
html_text = re.sub(r'{{(\s+\S+\s+)}}', '{}', html_text)
with open(html_fpath, 'w') as f_html:
f_html.write(html_text)
meta_log.main_info(' Extended version of HTML-report (for all references and assemblies) is saved to ' + html_fpath)
def create_meta_report(results_dirpath, json_texts):
html_fpath = os.path.join(results_dirpath, report_fname)
if not os.path.isfile(html_fpath):
init(html_fpath, is_meta=True)
from quast_libs import search_references_meta
taxons_for_krona = search_references_meta.taxons_for_krona
meta_log = get_logger(qconfig.LOGGER_META_NAME)
if taxons_for_krona:
create_krona_charts(taxons_for_krona, meta_log, results_dirpath,
json_texts)
# reading html template file
with open(html_fpath) as f_html:
html_text = f_html.read()
keyword = 'totalReport'
html_text = re.sub('{{ ' + keyword + ' }}',
'[' + ','.join(json_texts) + ']', html_text)
html_text = re.sub(r'{{(\s+\S+\s+)}}', '{}', html_text)
with open(html_fpath, 'w') as f_html:
f_html.write(html_text)
meta_log.main_info(
' Extended version of HTML-report (for all references and assemblies) is saved to '
+ html_fpath)
############################################################################
# Copyright (c) 2015-2020 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
from quast_libs import qconfig
from quast_libs.ca_utils.misc import is_same_reference, get_ref_by_chromosome, parse_cs_tag
from quast_libs.log import get_logger
logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
from quast_libs.qutils import correct_name
class Misassembly:
LOCAL = 0
INVERSION = 1
RELOCATION = 2
TRANSLOCATION = 3
INTERSPECTRANSLOCATION = 4 # for metaquast, if translocation occurs between chromosomes of different references
SCAFFOLD_GAP = 5
LOCAL_SCAFFOLD_GAP = 6
FRAGMENTED = 7
POTENTIALLY_MIS_CONTIGS = 8
POSSIBLE_MISASSEMBLIES = 9
MATCHED_SV = 10
POTENTIAL_MGE = 11
from quast_libs.site_packages.ordered_dict import OrderedDict
from quast_libs import qconfig
qconfig.check_python_version()
from site import addsitedir
addsitedir(os.path.join(qconfig.LIBS_LOCATION, 'site_packages'))
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, prepare_regular_quast_args
from quast_libs import contigs_analyzer, search_references_meta, plotter_data, qutils
from quast_libs.qutils import cleanup, check_dirpath, is_python2, run_parallel
from quast_libs.log import get_logger
logger = get_logger(qconfig.LOGGER_META_NAME)
logger.set_up_console_handler()
def _start_quast_main(args, assemblies, reference_fpath=None, output_dirpath=None, num_notifications_tuple=None,
labels=None, run_regular_quast=False, is_combined_ref=False, is_parallel_run=False):
args = args[:]
args.extend([asm.fpath for asm in assemblies])
if reference_fpath:
args.append('-R')
args.append(reference_fpath)
if output_dirpath:
args.append('-o')
from __future__ import with_statement
import os
import glob
import shutil
import tempfile
from quast_libs import reporting, qconfig, qutils
from quast_libs.ca_utils.misc import open_gzipsafe
from quast_libs.fastaparser import write_fasta
from quast_libs.genes_parser import Gene
from quast_libs.log import get_logger
from quast_libs.qutils import is_python2
logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
LICENSE_LIMITATIONS_MODE = False
OUTPUT_FASTA = False # whether output only .gff or with corresponding .fasta files
def gc_content(sequence):
GC_count = sequence.count('G') + sequence.count('C')
ACGT_length = len(sequence) - sequence.count('N')
if not ACGT_length:
return 0
return 100 * GC_count / ACGT_length
def gmhmm_p(tool_exec, fasta_fpath, heu_fpath, out_fpath, err_file, index):
""" Run GeneMark.hmm with this heuristic model (heu_dirpath)
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'))
def _start_quast_main(args, assemblies, reference_fpath=None, output_dirpath=None,
num_notifications_tuple=None, is_first_run=None, run_regular_quast=False):
args = args[:]
args.extend([asm.fpath for asm in assemblies])
if reference_fpath:
args.append('-R')
args.append(reference_fpath)
# axis params:
logarithmic_x_scale = False # for cumulative plots only
####################################################################################
######################## END OF CONFIGURABLE PARAMETERS ##########################
####################################################################################
import math
import sys
from quast_libs import fastaparser, qconfig, reporting
from quast_libs.log import get_logger, get_main_logger
from quast_libs.qutils import label_from_fpath, parse_str_to_num, run_parallel
from quast_libs.plotter_data import get_color_and_ls, colors
main_logger = get_main_logger()
logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
meta_logger = get_logger(qconfig.LOGGER_META_NAME)
# checking if matplotlib is installed
can_draw_plots = False
if qconfig.draw_plots:
try:
import matplotlib
matplotlib.use('Agg') # non-GUI backend
if matplotlib.__version__.startswith(
'0') or matplotlib.__version__.startswith('1.0'):
main_logger.info('')
main_logger.warning(
'Can\'t draw plots: matplotlib version is old! Please use matplotlib version 1.1 or higher.'
)
else:
# axis params:
logarithmic_x_scale = False # for cumulative plots only
####################################################################################
######################## END OF CONFIGURABLE PARAMETERS ##########################
####################################################################################
import os
import itertools
from quast_libs import fastaparser, qutils
from quast_libs import qconfig
from quast_libs.log import get_logger, get_main_logger
main_logger = get_main_logger()
logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
meta_logger = get_logger(qconfig.LOGGER_META_NAME)
from . import reporting
# checking if matplotlib is installed
can_draw_plots = True
if qconfig.draw_plots:
try:
import matplotlib
matplotlib.use('Agg') # non-GUI backend
if matplotlib.__version__.startswith('0') or matplotlib.__version__.startswith('1.0'):
main_logger.info('')
main_logger.warning('Can\'t draw plots: matplotlib version is old! Please use matplotlib version 1.1 or higher.')
can_draw_plots = False
# additionally check other imports