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)