def correct_assemblies(contigs_fpaths, output_dirpath, labels):
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
# we need correction but do not need min-contig filtration
min_contig = qconfig.min_contig
qconfig.min_contig = 0
corrected_contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting=None)
qconfig.min_contig = min_contig
assemblies = [Assembly(fpath, qutils.label_from_fpath(fpath)) for fpath in old_contigs_fpaths]
corrected_labels = [asm.label for asm in assemblies]
if qconfig.draw_plots or qconfig.html_report:
corr_fpaths = [asm.fpath for asm in assemblies]
corr_labels = [asm.label for asm in assemblies]
plotter_data.save_colors_and_ls(corr_fpaths, labels=corr_labels)
return assemblies, corrected_labels
def correct_assemblies(contigs_fpaths, output_dirpath, labels):
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
# we need correction but do not need min-contig filtration
min_contig = qconfig.min_contig
qconfig.min_contig = 0
corrected_contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting=None)
qconfig.min_contig = min_contig
assemblies = [Assembly(fpath, qutils.label_from_fpath(fpath)) for fpath in old_contigs_fpaths]
corrected_labels = [asm.label for asm in assemblies]
if qconfig.draw_plots or qconfig.html_report:
corr_fpaths = [asm.fpath for asm in assemblies]
corr_labels = [asm.label for asm in assemblies]
plotter_data.save_colors_and_ls(corr_fpaths, labels=corr_labels)
return assemblies, corrected_labels
def main(args):
check_dirpath(
qconfig.QUAST_HOME,
'You are trying to run it from ' + str(qconfig.QUAST_HOME) + '\n.' +
'Please, put QUAST in a different directory, then try again.\n',
exit_code=3)
if not args:
qconfig.usage(stream=sys.stderr)
sys.exit(1)
try:
import imp
imp.reload(qconfig)
imp.reload(qutils)
except:
reload(qconfig)
reload(qutils)
try:
locale.setlocale(locale.LC_ALL, 'en_US.utf8')
except Exception:
try:
locale.setlocale(locale.LC_ALL, 'en_US.UTF-8')
except Exception:
logger.warning('Python locale settings can\'t be changed')
quast_path = [os.path.realpath(__file__)]
quast_py_args, contigs_fpaths = parse_options(logger, quast_path + args)
output_dirpath, ref_fpath, labels = qconfig.output_dirpath, qconfig.reference, qconfig.labels
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
logger.main_info()
logger.print_params()
########################################################################
from quast_libs import reporting
reports = reporting.reports
try:
import imp
imp.reload(reporting)
except:
reload(reporting)
reporting.reports = reports
reporting.assembly_fpaths = []
from quast_libs import plotter # Do not remove this line! It would lead to a warning in matplotlib.
if qconfig.is_combined_ref:
corrected_dirpath = os.path.join(output_dirpath, '..',
qconfig.corrected_dirname)
else:
if os.path.isdir(corrected_dirpath):
shutil.rmtree(corrected_dirpath)
os.mkdir(corrected_dirpath)
qconfig.set_max_threads(logger)
check_reads_fpaths(logger)
# PROCESSING REFERENCE
if ref_fpath:
logger.main_info()
logger.main_info('Reference:')
original_ref_fpath = ref_fpath
ref_fpath = qutils.correct_reference(ref_fpath, corrected_dirpath)
if qconfig.optimal_assembly:
if not qconfig.pacbio_reads and not qconfig.nanopore_reads and not qconfig.mate_pairs:
logger.warning(
'Optimal assembly cannot be created. It requires mate-pairs or long reads (Pacbio SMRT or Oxford Nanopore).'
)
else:
optimal_assembly_fpath = optimal_assembly.do(
ref_fpath, original_ref_fpath,
os.path.join(output_dirpath,
qconfig.optimal_assembly_basename))
if optimal_assembly_fpath is not None:
contigs_fpaths.insert(0, optimal_assembly_fpath)
labels.insert(0, 'Optimal')
labels = qutils.process_labels(contigs_fpaths, labels)
else:
ref_fpath = ''
# PROCESSING CONTIGS
logger.main_info()
logger.main_info('Contigs:')
contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(
contigs_fpaths, corrected_dirpath, labels, reporting)
for contigs_fpath in contigs_fpaths:
report = reporting.get(contigs_fpath)
report.add_field(reporting.Fields.NAME,
qutils.label_from_fpath(contigs_fpath))
qconfig.assemblies_num = len(contigs_fpaths)
cov_fpath = qconfig.cov_fpath
physical_cov_fpath = qconfig.phys_cov_fpath
if qconfig.reads_fpaths or qconfig.reference_sam or qconfig.reference_sam or qconfig.sam_fpaths or qconfig.bam_fpaths:
bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(
ref_fpath,
contigs_fpaths,
os.path.join(output_dirpath, qconfig.reads_stats_dirname),
external_logger=logger)
qconfig.bed = bed_fpath
if not contigs_fpaths:
logger.error(
"None of the assembly files contains correct contigs. "
"Please, provide different files or decrease --min-contig threshold.",
fake_if_nested_run=True)
return 4
if qconfig.used_colors and qconfig.used_ls:
for i, label in enumerate(labels):
plotter_data.dict_color_and_ls[label] = (qconfig.used_colors[i],
qconfig.used_ls[i])
qconfig.assemblies_fpaths = contigs_fpaths
# Where all pdfs will be saved
all_pdf_fpath = None
if qconfig.draw_plots and plotter.can_draw_plots:
all_pdf_fpath = os.path.join(output_dirpath, qconfig.plots_fname)
if qconfig.json_output_dirpath:
from quast_libs.html_saver import json_saver
if json_saver.simplejson_error:
qconfig.json_output_dirpath = None
########################################################################
### Stats and plots
########################################################################
from quast_libs import basic_stats
icarus_gc_fpath, circos_gc_fpath = basic_stats.do(
ref_fpath, contigs_fpaths, os.path.join(output_dirpath, 'basic_stats'),
output_dirpath)
if qconfig.large_genome and ref_fpath:
unique_kmers.do(os.path.join(output_dirpath, 'basic_stats'), ref_fpath,
contigs_fpaths, logger)
aligned_contigs_fpaths = []
aligned_lengths_lists = []
contig_alignment_plot_fpath = None
icarus_html_fpath = None
circos_png_fpath = None
if ref_fpath:
########################################################################
### former PLANTAKOLYA, PLANTAGORA
########################################################################
from quast_libs import contigs_analyzer
is_cyclic = qconfig.prokaryote and not qconfig.check_for_fragmented_ref
aligner_statuses, aligned_lengths_per_fpath = contigs_analyzer.do(
ref_fpath, contigs_fpaths, is_cyclic,
os.path.join(output_dirpath, 'contigs_reports'),
old_contigs_fpaths, qconfig.bed)
for contigs_fpath in contigs_fpaths:
if aligner_statuses[
contigs_fpath] == contigs_analyzer.AlignerStatus.OK:
aligned_contigs_fpaths.append(contigs_fpath)
aligned_lengths_lists.append(
aligned_lengths_per_fpath[contigs_fpath])
# Before continue evaluating, check if aligner didn't skip all of the contigs files.
detailed_contigs_reports_dirpath = None
features_containers = None
if len(aligned_contigs_fpaths) and ref_fpath:
detailed_contigs_reports_dirpath = os.path.join(
output_dirpath, 'contigs_reports')
########################################################################
### NAx and NGAx ("aligned Nx and NGx")
########################################################################
from quast_libs import aligned_stats
aligned_stats.do(ref_fpath, aligned_contigs_fpaths, output_dirpath,
aligned_lengths_lists,
os.path.join(output_dirpath, 'aligned_stats'))
########################################################################
### GENOME_ANALYZER
########################################################################
from quast_libs import genome_analyzer
features_containers = genome_analyzer.do(
ref_fpath, aligned_contigs_fpaths, output_dirpath,
qconfig.features, qconfig.operons,
detailed_contigs_reports_dirpath,
os.path.join(output_dirpath, 'genome_stats'))
genes_by_labels = None
if qconfig.gene_finding:
if qconfig.glimmer:
########################################################################
### Glimmer
########################################################################
from quast_libs import glimmer
genes_by_labels = glimmer.do(
contigs_fpaths, qconfig.genes_lengths,
os.path.join(output_dirpath, 'predicted_genes'))
if not qconfig.glimmer or qconfig.test:
########################################################################
### GeneMark
########################################################################
from quast_libs import genemark
genes_by_labels = genemark.do(
contigs_fpaths, qconfig.genes_lengths,
os.path.join(output_dirpath, 'predicted_genes'),
qconfig.prokaryote, qconfig.metagenemark)
else:
logger.main_info("")
logger.notice(
"Genes are not predicted by default. Use --gene-finding option to enable it."
)
if qconfig.rna_gene_finding:
run_barrnap.do(contigs_fpaths,
os.path.join(output_dirpath, 'predicted_genes'), logger)
if qconfig.run_busco and not qconfig.is_combined_ref:
if qconfig.platform_name == 'macosx':
logger.main_info("")
logger.warning("BUSCO can be run on Linux only")
elif sys.version[0:3] == '2.5':
logger.main_info("")
logger.warning(
"BUSCO does not support Python versions older than 2.6.")
else:
from quast_libs import run_busco
run_busco.do(contigs_fpaths,
os.path.join(output_dirpath, qconfig.busco_dirname),
logger)
########################################################################
reports_fpaths, transposed_reports_fpaths = reporting.save_total(
output_dirpath)
########################################################################
### LARGE DRAWING TASKS
########################################################################
if qconfig.draw_plots or qconfig.create_icarus_html:
logger.print_timestamp()
logger.main_info('Creating large visual summaries...')
logger.main_info(
'This may take a while: press Ctrl-C to skip this step..')
try:
if detailed_contigs_reports_dirpath:
report_for_icarus_fpath_pattern = os.path.join(
detailed_contigs_reports_dirpath,
qconfig.icarus_report_fname_pattern)
stdout_pattern = os.path.join(
detailed_contigs_reports_dirpath,
qconfig.contig_report_fname_pattern)
else:
report_for_icarus_fpath_pattern = None
stdout_pattern = None
draw_alignment_plots = qconfig.draw_svg or qconfig.create_icarus_html
draw_circos_plot = qconfig.draw_plots and ref_fpath and len(
aligned_contigs_fpaths) and not qconfig.space_efficient
number_of_steps = sum([
int(bool(value)) for value in
[draw_alignment_plots, draw_circos_plot, all_pdf_fpath]
])
if draw_alignment_plots:
########################################################################
### VISUALIZE CONTIG ALIGNMENT
########################################################################
logger.main_info(' 1 of %d: Creating Icarus viewers...' %
number_of_steps)
from quast_libs import icarus
icarus_html_fpath, contig_alignment_plot_fpath = icarus.do(
contigs_fpaths,
report_for_icarus_fpath_pattern,
output_dirpath,
ref_fpath,
stdout_pattern=stdout_pattern,
features=features_containers,
cov_fpath=cov_fpath,
physical_cov_fpath=physical_cov_fpath,
gc_fpath=icarus_gc_fpath,
json_output_dir=qconfig.json_output_dirpath,
genes_by_labels=genes_by_labels)
if draw_circos_plot:
logger.main_info(
' %d of %d: Creating Circos plots...' %
(2 if draw_alignment_plots else 1, number_of_steps))
from quast_libs import circos
circos_png_fpath, circos_legend_fpath = circos.do(
ref_fpath, contigs_fpaths, report_for_icarus_fpath_pattern,
circos_gc_fpath, features_containers, cov_fpath,
os.path.join(output_dirpath, 'circos'), logger)
if all_pdf_fpath:
# full report in PDF format: all tables and plots
logger.main_info(
' %d of %d: Creating PDF with all tables and plots...' %
(number_of_steps, number_of_steps))
plotter.fill_all_pdf_file(all_pdf_fpath)
logger.main_info('Done')
except KeyboardInterrupt:
logger.main_info('..step skipped!')
if all_pdf_fpath and os.path.isfile(all_pdf_fpath):
os.remove(all_pdf_fpath)
########################################################################
### TOTAL REPORT
########################################################################
logger.print_timestamp()
logger.main_info('RESULTS:')
logger.main_info(' Text versions of total report are saved to ' +
reports_fpaths)
logger.main_info(
' Text versions of transposed total report are saved to ' +
transposed_reports_fpaths)
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_colors(output_dirpath, contigs_fpaths,
plotter_data.dict_color_and_ls)
html_saver.save_total_report(output_dirpath, qconfig.min_contig,
ref_fpath)
if all_pdf_fpath and os.path.isfile(all_pdf_fpath):
logger.main_info(' PDF version (tables and plots) is saved to ' +
all_pdf_fpath)
if circos_png_fpath:
logger.main_info(
' Circos plot is saved to %s (the annotation is in %s). Circos configuration file is saved to %s'
% (circos_png_fpath, circos_legend_fpath,
circos_png_fpath.replace('.png', '.conf')))
if icarus_html_fpath:
logger.main_info(' Icarus (contig browser) is saved to %s' %
icarus_html_fpath)
if qconfig.draw_svg and contig_alignment_plot_fpath:
logger.main_info(' Contig alignment plot is saved to %s' %
contig_alignment_plot_fpath)
cleanup(corrected_dirpath)
return logger.finish_up(check_test=qconfig.test)
def main(args):
check_dirpath(qconfig.QUAST_HOME, 'You are trying to run it from ' + str(qconfig.QUAST_HOME) + '\n.' +
'Please, put QUAST in a different directory, then try again.\n', exit_code=3)
if not args:
qconfig.usage(stream=sys.stderr)
sys.exit(1)
try:
import imp
imp.reload(qconfig)
imp.reload(qutils)
except:
reload(qconfig)
reload(qutils)
try:
locale.setlocale(locale.LC_ALL, 'en_US.utf8')
except Exception:
try:
locale.setlocale(locale.LC_ALL, 'en_US.UTF-8')
except Exception:
logger.warning('Python locale settings can\'t be changed')
quast_path = [os.path.realpath(__file__)]
quast_py_args, contigs_fpaths = parse_options(logger, quast_path + args)
output_dirpath, ref_fpath, labels = qconfig.output_dirpath, qconfig.reference, qconfig.labels
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
logger.main_info()
logger.print_params()
########################################################################
from quast_libs import reporting
reports = reporting.reports
try:
import imp
imp.reload(reporting)
except:
reload(reporting)
reporting.reports = reports
reporting.assembly_fpaths = []
from quast_libs import plotter # Do not remove this line! It would lead to a warning in matplotlib.
if qconfig.is_combined_ref:
corrected_dirpath = os.path.join(output_dirpath, '..', qconfig.corrected_dirname)
else:
if os.path.isdir(corrected_dirpath):
shutil.rmtree(corrected_dirpath)
os.mkdir(corrected_dirpath)
qconfig.set_max_threads(logger)
check_reads_fpaths(logger)
# PROCESSING REFERENCE
if ref_fpath:
logger.main_info()
logger.main_info('Reference:')
original_ref_fpath = ref_fpath
ref_fpath = qutils.correct_reference(ref_fpath, corrected_dirpath)
if qconfig.ideal_assembly:
ideal_assembly_fpath = ideal_assembly.do(ref_fpath, original_ref_fpath,
os.path.join(output_dirpath, qconfig.ideal_assembly_basename))
if ideal_assembly_fpath is not None:
contigs_fpaths.insert(0, ideal_assembly_fpath)
labels.insert(0, 'IDEAL ASSEMBLY')
labels = qutils.process_labels(contigs_fpaths, labels)
else:
ref_fpath = ''
# PROCESSING CONTIGS
logger.main_info()
logger.main_info('Contigs:')
contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting)
for contigs_fpath in contigs_fpaths:
report = reporting.get(contigs_fpath)
report.add_field(reporting.Fields.NAME, qutils.label_from_fpath(contigs_fpath))
qconfig.assemblies_num = len(contigs_fpaths)
cov_fpath = qconfig.cov_fpath
physical_cov_fpath = qconfig.phys_cov_fpath
if qconfig.reads_fpaths or qconfig.reference_sam or qconfig.reference_sam or qconfig.sam_fpaths or qconfig.bam_fpaths:
bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(ref_fpath, contigs_fpaths,
os.path.join(output_dirpath, qconfig.reads_stats_dirname),
external_logger=logger)
qconfig.bed = bed_fpath
if not contigs_fpaths:
logger.error("None of the assembly files contains correct contigs. "
"Please, provide different files or decrease --min-contig threshold.",
fake_if_nested_run=True)
return 4
if qconfig.used_colors and qconfig.used_ls:
for i, label in enumerate(labels):
plotter_data.dict_color_and_ls[label] = (qconfig.used_colors[i], qconfig.used_ls[i])
qconfig.assemblies_fpaths = contigs_fpaths
# Where all pdfs will be saved
all_pdf_fpath = None
if qconfig.draw_plots and plotter.can_draw_plots:
all_pdf_fpath = os.path.join(output_dirpath, qconfig.plots_fname)
if qconfig.json_output_dirpath:
from quast_libs.html_saver import json_saver
if json_saver.simplejson_error:
qconfig.json_output_dirpath = None
########################################################################
### Stats and plots
########################################################################
from quast_libs import basic_stats
icarus_gc_fpath, circos_gc_fpath = basic_stats.do(ref_fpath, contigs_fpaths, os.path.join(output_dirpath, 'basic_stats'), output_dirpath)
if qconfig.large_genome and ref_fpath:
unique_kmers.do(os.path.join(output_dirpath, 'basic_stats'), ref_fpath, contigs_fpaths, logger)
aligned_contigs_fpaths = []
aligned_lengths_lists = []
contig_alignment_plot_fpath = None
icarus_html_fpath = None
circos_png_fpath = None
if ref_fpath:
########################################################################
### former PLANTAKOLYA, PLANTAGORA
########################################################################
from quast_libs import contigs_analyzer
is_cyclic = qconfig.prokaryote and not qconfig.check_for_fragmented_ref
nucmer_statuses, aligned_lengths_per_fpath = contigs_analyzer.do(
ref_fpath, contigs_fpaths, is_cyclic, os.path.join(output_dirpath, 'contigs_reports'),
old_contigs_fpaths, qconfig.bed)
for contigs_fpath in contigs_fpaths:
if nucmer_statuses[contigs_fpath] == contigs_analyzer.NucmerStatus.OK:
aligned_contigs_fpaths.append(contigs_fpath)
aligned_lengths_lists.append(aligned_lengths_per_fpath[contigs_fpath])
# Before continue evaluating, check if nucmer didn't skip all of the contigs files.
detailed_contigs_reports_dirpath = None
features_containers = None
if len(aligned_contigs_fpaths) and ref_fpath:
detailed_contigs_reports_dirpath = os.path.join(output_dirpath, 'contigs_reports')
########################################################################
### NAx and NGAx ("aligned Nx and NGx")
########################################################################
from quast_libs import aligned_stats
aligned_stats.do(
ref_fpath, aligned_contigs_fpaths, output_dirpath,
aligned_lengths_lists, os.path.join(output_dirpath, 'aligned_stats'))
########################################################################
### GENOME_ANALYZER
########################################################################
from quast_libs import genome_analyzer
features_containers = genome_analyzer.do(
ref_fpath, aligned_contigs_fpaths, output_dirpath,
qconfig.genes, qconfig.operons, detailed_contigs_reports_dirpath,
os.path.join(output_dirpath, 'genome_stats'))
genes_by_labels = None
if qconfig.gene_finding:
if qconfig.glimmer:
########################################################################
### Glimmer
########################################################################
from quast_libs import glimmer
genes_by_labels = glimmer.do(contigs_fpaths, qconfig.genes_lengths, os.path.join(output_dirpath, 'predicted_genes'))
if not qconfig.glimmer or qconfig.test:
########################################################################
### GeneMark
########################################################################
from quast_libs import genemark
genes_by_labels = genemark.do(contigs_fpaths, qconfig.genes_lengths, os.path.join(output_dirpath, 'predicted_genes'),
qconfig.prokaryote, qconfig.metagenemark)
else:
logger.main_info("")
logger.notice("Genes are not predicted by default. Use --gene-finding option to enable it.")
if qconfig.rna_gene_finding:
run_barrnap.do(contigs_fpaths, os.path.join(output_dirpath, 'predicted_genes'), logger)
if qconfig.run_busco and not qconfig.is_combined_ref:
if qconfig.platform_name == 'macosx':
logger.main_info("")
logger.warning("BUSCO can be run on Linux only")
elif sys.version[0:3] == '2.5':
logger.main_info("")
logger.warning("BUSCO does not support Python versions older than 2.6.")
else:
from quast_libs import run_busco
run_busco.do(contigs_fpaths, os.path.join(output_dirpath, qconfig.busco_dirname), logger)
########################################################################
reports_fpaths, transposed_reports_fpaths = reporting.save_total(output_dirpath)
########################################################################
### LARGE DRAWING TASKS
########################################################################
if qconfig.draw_plots or qconfig.create_icarus_html:
logger.print_timestamp()
logger.main_info('Creating large visual summaries...')
logger.main_info('This may take a while: press Ctrl-C to skip this step..')
try:
if detailed_contigs_reports_dirpath:
report_for_icarus_fpath_pattern = os.path.join(detailed_contigs_reports_dirpath, qconfig.icarus_report_fname_pattern)
stdout_pattern = os.path.join(detailed_contigs_reports_dirpath, qconfig.contig_report_fname_pattern)
else:
report_for_icarus_fpath_pattern = None
stdout_pattern = None
draw_alignment_plots = qconfig.draw_svg or qconfig.create_icarus_html
draw_circos_plot = qconfig.draw_plots and ref_fpath and len(aligned_contigs_fpaths) and not qconfig.space_efficient
number_of_steps = sum([int(bool(value)) for value in [draw_alignment_plots, draw_circos_plot, all_pdf_fpath]])
if draw_alignment_plots:
########################################################################
### VISUALIZE CONTIG ALIGNMENT
########################################################################
logger.main_info(' 1 of %d: Creating Icarus viewers...' % number_of_steps)
from quast_libs import icarus
icarus_html_fpath, contig_alignment_plot_fpath = icarus.do(
contigs_fpaths, report_for_icarus_fpath_pattern, output_dirpath, ref_fpath,
stdout_pattern=stdout_pattern, features=features_containers,
cov_fpath=cov_fpath, physical_cov_fpath=physical_cov_fpath, gc_fpath=icarus_gc_fpath,
json_output_dir=qconfig.json_output_dirpath, genes_by_labels=genes_by_labels)
if draw_circos_plot:
logger.main_info(' %d of %d: Creating Circos plots...' % (2 if draw_alignment_plots else 1, number_of_steps))
from quast_libs import circos
circos_png_fpath, circos_legend_fpath = circos.do(ref_fpath, contigs_fpaths, report_for_icarus_fpath_pattern, circos_gc_fpath,
features_containers, cov_fpath, os.path.join(output_dirpath, 'circos'), logger)
if all_pdf_fpath:
# full report in PDF format: all tables and plots
logger.main_info(' %d of %d: Creating PDF with all tables and plots...' % (number_of_steps, number_of_steps))
plotter.fill_all_pdf_file(all_pdf_fpath)
logger.main_info('Done')
except KeyboardInterrupt:
logger.main_info('..step skipped!')
if all_pdf_fpath and os.path.isfile(all_pdf_fpath):
os.remove(all_pdf_fpath)
########################################################################
### TOTAL REPORT
########################################################################
logger.print_timestamp()
logger.main_info('RESULTS:')
logger.main_info(' Text versions of total report are saved to ' + reports_fpaths)
logger.main_info(' Text versions of transposed total report are saved to ' + transposed_reports_fpaths)
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_colors(output_dirpath, contigs_fpaths, plotter_data.dict_color_and_ls)
html_saver.save_total_report(output_dirpath, qconfig.min_contig, ref_fpath)
if all_pdf_fpath and os.path.isfile(all_pdf_fpath):
logger.main_info(' PDF version (tables and plots) is saved to ' + all_pdf_fpath)
if circos_png_fpath:
logger.main_info(' Circos plot is saved to %s (the annotation is in %s). Circos configuration file is saved to %s' %
(circos_png_fpath, circos_legend_fpath, circos_png_fpath.replace('.png', '.conf')))
if icarus_html_fpath:
logger.main_info(' Icarus (contig browser) is saved to %s' % icarus_html_fpath)
if qconfig.draw_svg and contig_alignment_plot_fpath:
logger.main_info(' Contig alignment plot is saved to %s' % contig_alignment_plot_fpath)
cleanup(corrected_dirpath)
return logger.finish_up(check_test=qconfig.test)
def main(args):
if ' ' in qconfig.QUAST_HOME:
logger.error('QUAST does not support spaces in paths. \n'
'You are trying to run it from ' + str(qconfig.QUAST_HOME) + '\n'
'Please, put QUAST in a different directory, then try again.\n',
to_stderr=True,
exit_with_code=3)
if not args:
qconfig.usage()
sys.exit(0)
reload(qconfig)
quast_path = [os.path.realpath(__file__)]
quast_py_args, contigs_fpaths = parse_options(logger, quast_path + args)
output_dirpath, ref_fpath, labels = qconfig.output_dirpath, qconfig.reference, qconfig.labels
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
logger.main_info()
logger.print_params()
########################################################################
from quast_libs import reporting
reports = reporting.reports
reload(reporting)
reporting.reports = reports
reporting.assembly_fpaths = []
from quast_libs import plotter # Do not remove this line! It would lead to a warning in matplotlib.
if qconfig.is_combined_ref:
corrected_dirpath = os.path.join(output_dirpath, '..', qconfig.corrected_dirname)
else:
if os.path.isdir(corrected_dirpath):
shutil.rmtree(corrected_dirpath)
os.mkdir(corrected_dirpath)
# PROCESSING REFERENCE
if ref_fpath:
logger.main_info()
logger.main_info('Reference:')
ref_fpath = qutils.correct_reference(ref_fpath, corrected_dirpath)
else:
ref_fpath = ''
# PROCESSING CONTIGS
logger.main_info()
logger.main_info('Contigs:')
contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting)
for contigs_fpath in contigs_fpaths:
report = reporting.get(contigs_fpath)
report.add_field(reporting.Fields.NAME, qutils.label_from_fpath(contigs_fpath))
qconfig.assemblies_num = len(contigs_fpaths)
reads_fpaths = []
cov_fpath = []
physical_cov_fpath = []
if qconfig.forward_reads:
reads_fpaths.append(qconfig.forward_reads)
if qconfig.reverse_reads:
reads_fpaths.append(qconfig.reverse_reads)
if (reads_fpaths or qconfig.sam or qconfig.bam) and ref_fpath:
bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(ref_fpath, contigs_fpaths, reads_fpaths, None,
os.path.join(output_dirpath, qconfig.variation_dirname),
external_logger=logger, sam_fpath=qconfig.sam, bam_fpath=qconfig.bam, bed_fpath=qconfig.bed)
qconfig.bed = bed_fpath
if not contigs_fpaths:
logger.error("None of the assembly files contains correct contigs. "
"Please, provide different files or decrease --min-contig threshold.",
fake_if_nested_run=True)
return 4
if qconfig.used_colors and qconfig.used_ls:
for i, label in enumerate(labels):
plotter.dict_color_and_ls[label] = (qconfig.used_colors[i], qconfig.used_ls[i])
qconfig.assemblies_fpaths = contigs_fpaths
if qconfig.with_gage:
########################################################################
### GAGE
########################################################################
if not ref_fpath:
logger.warning("GAGE can't be run without a reference and will be skipped.")
else:
from quast_libs import gage
gage.do(ref_fpath, contigs_fpaths, output_dirpath)
# Where all pdfs will be saved
all_pdf_fpath = os.path.join(output_dirpath, qconfig.plots_fname)
all_pdf_file = None
if qconfig.draw_plots and plotter.can_draw_plots:
try:
from matplotlib.backends.backend_pdf import PdfPages
all_pdf_file = PdfPages(all_pdf_fpath)
except:
all_pdf_file = None
if qconfig.json_output_dirpath:
from quast_libs.html_saver import json_saver
if json_saver.simplejson_error:
json_output_dirpath = None
########################################################################
### Stats and plots
########################################################################
from quast_libs import basic_stats
basic_stats.do(ref_fpath, contigs_fpaths, os.path.join(output_dirpath, 'basic_stats'),
qconfig.json_output_dirpath, output_dirpath)
aligned_contigs_fpaths = []
aligned_lengths_lists = []
contig_alignment_plot_fpath = None
icarus_html_fpath = None
if ref_fpath:
########################################################################
### former PLANTAKOLYA, PLANTAGORA
########################################################################
from quast_libs import contigs_analyzer
nucmer_statuses, aligned_lengths_per_fpath = contigs_analyzer.do(
ref_fpath, contigs_fpaths, qconfig.prokaryote, os.path.join(output_dirpath, 'contigs_reports'),
old_contigs_fpaths, qconfig.bed)
for contigs_fpath in contigs_fpaths:
if nucmer_statuses[contigs_fpath] == contigs_analyzer.NucmerStatus.OK:
aligned_contigs_fpaths.append(contigs_fpath)
aligned_lengths_lists.append(aligned_lengths_per_fpath[contigs_fpath])
# Before continue evaluating, check if nucmer didn't skip all of the contigs files.
detailed_contigs_reports_dirpath = None
features_containers = None
if len(aligned_contigs_fpaths) and ref_fpath:
detailed_contigs_reports_dirpath = os.path.join(output_dirpath, 'contigs_reports')
########################################################################
### NAx and NGAx ("aligned Nx and NGx")
########################################################################
from quast_libs import aligned_stats
aligned_stats.do(
ref_fpath, aligned_contigs_fpaths, output_dirpath, qconfig.json_output_dirpath,
aligned_lengths_lists, os.path.join(output_dirpath, 'aligned_stats'))
########################################################################
### GENOME_ANALYZER
########################################################################
from quast_libs import genome_analyzer
features_containers = genome_analyzer.do(
ref_fpath, aligned_contigs_fpaths, output_dirpath, qconfig.json_output_dirpath,
qconfig.genes, qconfig.operons, detailed_contigs_reports_dirpath,
os.path.join(output_dirpath, 'genome_stats'))
genes_by_labels = None
if qconfig.gene_finding:
if qconfig.glimmer:
########################################################################
### Glimmer
########################################################################
from quast_libs import glimmer
genes_by_labels = glimmer.do(contigs_fpaths, qconfig.genes_lengths, os.path.join(output_dirpath, 'predicted_genes'))
else:
########################################################################
### GeneMark
########################################################################
from quast_libs import genemark
genes_by_labels = genemark.do(contigs_fpaths, qconfig.genes_lengths, os.path.join(output_dirpath, 'predicted_genes'),
qconfig.prokaryote, qconfig.meta)
else:
logger.main_info("")
logger.notice("Genes are not predicted by default. Use --gene-finding option to enable it.")
########################################################################
reports_fpaths, transposed_reports_fpaths = reporting.save_total(output_dirpath)
########################################################################
### LARGE DRAWING TASKS
########################################################################
if qconfig.draw_plots or qconfig.create_icarus_html:
logger.print_timestamp()
logger.main_info('Creating large visual summaries...')
logger.main_info('This may take a while: press Ctrl-C to skip this step..')
try:
if detailed_contigs_reports_dirpath:
report_for_icarus_fpath_pattern = os.path.join(detailed_contigs_reports_dirpath, qconfig.icarus_report_fname_pattern)
stdout_pattern = os.path.join(detailed_contigs_reports_dirpath, qconfig.contig_report_fname_pattern)
else:
report_for_icarus_fpath_pattern = None
stdout_pattern = None
draw_alignment_plots = qconfig.draw_svg or qconfig.create_icarus_html
number_of_steps = sum([int(bool(value)) for value in [draw_alignment_plots, all_pdf_file]])
if draw_alignment_plots:
########################################################################
### VISUALIZE CONTIG ALIGNMENT
########################################################################
logger.main_info(' 1 of %d: Creating Icarus viewers...' % number_of_steps)
from quast_libs import icarus
icarus_html_fpath, contig_alignment_plot_fpath = icarus.do(
contigs_fpaths, report_for_icarus_fpath_pattern, output_dirpath, ref_fpath,
stdout_pattern=stdout_pattern, features=features_containers, cov_fpath=cov_fpath,
physical_cov_fpath=physical_cov_fpath, json_output_dir=qconfig.json_output_dirpath,
genes_by_labels=genes_by_labels)
if all_pdf_file:
# full report in PDF format: all tables and plots
logger.main_info(' %d of %d: Creating PDF with all tables and plots...' % (number_of_steps, number_of_steps))
plotter.fill_all_pdf_file(all_pdf_file)
logger.main_info('Done')
except KeyboardInterrupt:
logger.main_info('..step skipped!')
os.remove(all_pdf_fpath)
########################################################################
### TOTAL REPORT
########################################################################
logger.print_timestamp()
logger.main_info('RESULTS:')
logger.main_info(' Text versions of total report are saved to ' + reports_fpaths)
logger.main_info(' Text versions of transposed total report are saved to ' + transposed_reports_fpaths)
if qconfig.json_output_dirpath:
json_saver.save_total_report(qconfig.json_output_dirpath, qconfig.min_contig, ref_fpath)
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_colors(output_dirpath, contigs_fpaths, plotter.dict_color_and_ls)
html_saver.save_total_report(output_dirpath, qconfig.min_contig, ref_fpath)
if os.path.isfile(all_pdf_fpath):
logger.main_info(' PDF version (tables and plots) is saved to ' + all_pdf_fpath)
if icarus_html_fpath:
logger.main_info(' Icarus (contig browser) is saved to %s' % icarus_html_fpath)
if qconfig.draw_svg and contig_alignment_plot_fpath:
logger.main_info(' Contig alignment plot is saved to %s' % contig_alignment_plot_fpath)
cleanup(corrected_dirpath)
return logger.finish_up(check_test=qconfig.test)
def main(args):
check_dirpath(
qconfig.QUAST_HOME,
"You are trying to run it from "
+ str(qconfig.QUAST_HOME)
+ "\n."
+ "Please, put QUAST in a different directory, then try again.\n",
exit_code=3,
)
if not args:
qconfig.usage()
sys.exit(0)
try:
import imp
imp.reload(qconfig)
except:
reload(qconfig)
try:
locale.setlocale(locale.LC_ALL, "en_US.utf8")
except Exception:
try:
locale.setlocale(locale.LC_ALL, "en_US.UTF-8")
except Exception:
logger.warning("Python locale settings can't be changed")
quast_path = [os.path.realpath(__file__)]
quast_py_args, contigs_fpaths = parse_options(logger, quast_path + args)
output_dirpath, ref_fpath, labels = qconfig.output_dirpath, qconfig.reference, qconfig.labels
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
logger.main_info()
logger.print_params()
########################################################################
from quast_libs import reporting
reports = reporting.reports
try:
import imp
imp.reload(reporting)
except:
reload(reporting)
reporting.reports = reports
reporting.assembly_fpaths = []
from quast_libs import plotter # Do not remove this line! It would lead to a warning in matplotlib.
if qconfig.is_combined_ref:
corrected_dirpath = os.path.join(output_dirpath, "..", qconfig.corrected_dirname)
else:
if os.path.isdir(corrected_dirpath):
shutil.rmtree(corrected_dirpath)
os.mkdir(corrected_dirpath)
qconfig.set_max_threads(logger)
# PROCESSING REFERENCE
if ref_fpath:
logger.main_info()
logger.main_info("Reference:")
ref_fpath = qutils.correct_reference(ref_fpath, corrected_dirpath)
else:
ref_fpath = ""
# PROCESSING CONTIGS
logger.main_info()
logger.main_info("Contigs:")
contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting)
for contigs_fpath in contigs_fpaths:
report = reporting.get(contigs_fpath)
report.add_field(reporting.Fields.NAME, qutils.label_from_fpath(contigs_fpath))
qconfig.assemblies_num = len(contigs_fpaths)
reads_fpaths = []
cov_fpath = qconfig.cov_fpath
physical_cov_fpath = qconfig.phys_cov_fpath
if qconfig.forward_reads:
reads_fpaths.append(qconfig.forward_reads)
if qconfig.reverse_reads:
reads_fpaths.append(qconfig.reverse_reads)
if (reads_fpaths or qconfig.sam or qconfig.bam) and ref_fpath:
bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(
ref_fpath,
contigs_fpaths,
reads_fpaths,
None,
os.path.join(output_dirpath, qconfig.variation_dirname),
external_logger=logger,
sam_fpath=qconfig.sam,
bam_fpath=qconfig.bam,
bed_fpath=qconfig.bed,
)
qconfig.bed = bed_fpath
if not contigs_fpaths:
logger.error(
"None of the assembly files contains correct contigs. "
"Please, provide different files or decrease --min-contig threshold.",
fake_if_nested_run=True,
)
return 4
if qconfig.used_colors and qconfig.used_ls:
for i, label in enumerate(labels):
plotter.dict_color_and_ls[label] = (qconfig.used_colors[i], qconfig.used_ls[i])
qconfig.assemblies_fpaths = contigs_fpaths
# Where all pdfs will be saved
all_pdf_fpath = os.path.join(output_dirpath, qconfig.plots_fname)
all_pdf_file = None
if qconfig.draw_plots and plotter.can_draw_plots:
try:
from matplotlib.backends.backend_pdf import PdfPages
all_pdf_file = PdfPages(all_pdf_fpath)
except:
all_pdf_file = None
if qconfig.json_output_dirpath:
from quast_libs.html_saver import json_saver
if json_saver.simplejson_error:
json_output_dirpath = None
########################################################################
### Stats and plots
########################################################################
from quast_libs import basic_stats
basic_stats.do(
ref_fpath,
contigs_fpaths,
os.path.join(output_dirpath, "basic_stats"),
qconfig.json_output_dirpath,
output_dirpath,
)
aligned_contigs_fpaths = []
aligned_lengths_lists = []
contig_alignment_plot_fpath = None
icarus_html_fpath = None
if ref_fpath:
########################################################################
### former PLANTAKOLYA, PLANTAGORA
########################################################################
from quast_libs import contigs_analyzer
is_cyclic = qconfig.prokaryote and not qconfig.check_for_fragmented_ref
nucmer_statuses, aligned_lengths_per_fpath = contigs_analyzer.do(
ref_fpath,
contigs_fpaths,
is_cyclic,
os.path.join(output_dirpath, "contigs_reports"),
old_contigs_fpaths,
qconfig.bed,
)
for contigs_fpath in contigs_fpaths:
if nucmer_statuses[contigs_fpath] == contigs_analyzer.NucmerStatus.OK:
aligned_contigs_fpaths.append(contigs_fpath)
aligned_lengths_lists.append(aligned_lengths_per_fpath[contigs_fpath])
# Before continue evaluating, check if nucmer didn't skip all of the contigs files.
detailed_contigs_reports_dirpath = None
features_containers = None
if len(aligned_contigs_fpaths) and ref_fpath:
detailed_contigs_reports_dirpath = os.path.join(output_dirpath, "contigs_reports")
########################################################################
### NAx and NGAx ("aligned Nx and NGx")
########################################################################
from quast_libs import aligned_stats
aligned_stats.do(
ref_fpath,
aligned_contigs_fpaths,
output_dirpath,
qconfig.json_output_dirpath,
aligned_lengths_lists,
os.path.join(output_dirpath, "aligned_stats"),
)
########################################################################
### GENOME_ANALYZER
########################################################################
from quast_libs import genome_analyzer
features_containers = genome_analyzer.do(
ref_fpath,
aligned_contigs_fpaths,
output_dirpath,
qconfig.json_output_dirpath,
qconfig.genes,
qconfig.operons,
detailed_contigs_reports_dirpath,
os.path.join(output_dirpath, "genome_stats"),
)
if qconfig.with_gage:
########################################################################
### GAGE
########################################################################
if not ref_fpath:
logger.warning("GAGE can't be run without a reference and will be skipped.")
else:
from quast_libs import gage
gage.do(ref_fpath, contigs_fpaths, output_dirpath)
genes_by_labels = None
if qconfig.gene_finding:
if qconfig.glimmer:
########################################################################
### Glimmer
########################################################################
from quast_libs import glimmer
genes_by_labels = glimmer.do(
contigs_fpaths, qconfig.genes_lengths, os.path.join(output_dirpath, "predicted_genes")
)
else:
########################################################################
### GeneMark
########################################################################
from quast_libs import genemark
genes_by_labels = genemark.do(
contigs_fpaths,
qconfig.genes_lengths,
os.path.join(output_dirpath, "predicted_genes"),
qconfig.prokaryote,
qconfig.meta,
)
else:
logger.main_info("")
logger.notice("Genes are not predicted by default. Use --gene-finding option to enable it.")
########################################################################
reports_fpaths, transposed_reports_fpaths = reporting.save_total(output_dirpath)
########################################################################
### LARGE DRAWING TASKS
########################################################################
if qconfig.draw_plots or qconfig.create_icarus_html:
logger.print_timestamp()
logger.main_info("Creating large visual summaries...")
logger.main_info("This may take a while: press Ctrl-C to skip this step..")
try:
if detailed_contigs_reports_dirpath:
report_for_icarus_fpath_pattern = os.path.join(
detailed_contigs_reports_dirpath, qconfig.icarus_report_fname_pattern
)
stdout_pattern = os.path.join(detailed_contigs_reports_dirpath, qconfig.contig_report_fname_pattern)
else:
report_for_icarus_fpath_pattern = None
stdout_pattern = None
draw_alignment_plots = qconfig.draw_svg or qconfig.create_icarus_html
number_of_steps = sum([int(bool(value)) for value in [draw_alignment_plots, all_pdf_file]])
if draw_alignment_plots:
########################################################################
### VISUALIZE CONTIG ALIGNMENT
########################################################################
logger.main_info(" 1 of %d: Creating Icarus viewers..." % number_of_steps)
from quast_libs import icarus
icarus_html_fpath, contig_alignment_plot_fpath = icarus.do(
contigs_fpaths,
report_for_icarus_fpath_pattern,
output_dirpath,
ref_fpath,
stdout_pattern=stdout_pattern,
features=features_containers,
cov_fpath=cov_fpath,
physical_cov_fpath=physical_cov_fpath,
json_output_dir=qconfig.json_output_dirpath,
genes_by_labels=genes_by_labels,
)
if all_pdf_file:
# full report in PDF format: all tables and plots
logger.main_info(
" %d of %d: Creating PDF with all tables and plots..." % (number_of_steps, number_of_steps)
)
plotter.fill_all_pdf_file(all_pdf_file)
logger.main_info("Done")
except KeyboardInterrupt:
logger.main_info("..step skipped!")
os.remove(all_pdf_fpath)
########################################################################
### TOTAL REPORT
########################################################################
logger.print_timestamp()
logger.main_info("RESULTS:")
logger.main_info(" Text versions of total report are saved to " + reports_fpaths)
logger.main_info(" Text versions of transposed total report are saved to " + transposed_reports_fpaths)
if qconfig.json_output_dirpath:
json_saver.save_total_report(qconfig.json_output_dirpath, qconfig.min_contig, ref_fpath)
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_colors(output_dirpath, contigs_fpaths, plotter.dict_color_and_ls)
html_saver.save_total_report(output_dirpath, qconfig.min_contig, ref_fpath)
if os.path.isfile(all_pdf_fpath):
logger.main_info(" PDF version (tables and plots) is saved to " + all_pdf_fpath)
if icarus_html_fpath:
logger.main_info(" Icarus (contig browser) is saved to %s" % icarus_html_fpath)
if qconfig.draw_svg and contig_alignment_plot_fpath:
logger.main_info(" Contig alignment plot is saved to %s" % contig_alignment_plot_fpath)
cleanup(corrected_dirpath)
return logger.finish_up(check_test=qconfig.test)
