def do(ref_fpath, aligned_contigs_fpaths, output_dirpath, json_output_dirpath,
aligned_lengths_lists, aligned_stats_dirpath):
if not os.path.isdir(aligned_stats_dirpath):
os.mkdir(aligned_stats_dirpath)
########################################################################
report_dict = {'header': []}
for contigs_fpath in aligned_contigs_fpaths:
report_dict[qutils.name_from_fpath(contigs_fpath)] = []
########################################################################
logger.print_timestamp()
logger.main_info('Running NA-NGA calculation...')
ref_chr_lengths = fastaparser.get_chr_lengths_from_fastafile(ref_fpath)
reference_length = sum(ref_chr_lengths.values())
assembly_lengths = []
for contigs_fpath in aligned_contigs_fpaths:
assembly_lengths.append(sum(fastaparser.get_chr_lengths_from_fastafile(contigs_fpath).values()))
import N50
for i, (contigs_fpath, lens, assembly_len) in enumerate(
itertools.izip(aligned_contigs_fpaths, aligned_lengths_lists, assembly_lengths)):
na50 = N50.NG50(lens, assembly_len)
na75 = N50.NG50(lens, assembly_len, 75)
la50 = N50.LG50(lens, assembly_len)
la75 = N50.LG50(lens, assembly_len, 75)
if not qconfig.is_combined_ref:
nga50 = N50.NG50(lens, reference_length)
nga75 = N50.NG50(lens, reference_length, 75)
lga50 = N50.LG50(lens, reference_length)
lga75 = N50.LG50(lens, reference_length, 75)
logger.info(' ' +
qutils.index_to_str(i) +
qutils.label_from_fpath(contigs_fpath) +
', Largest alignment = ' + str(max(lens)) +
', NA50 = ' + str(na50) +
(', NGA50 = ' + str(nga50) if not qconfig.is_combined_ref and nga50 else '') +
', LA50 = ' + str(la50) +
(', LGA50 = ' + str(lga50) if not qconfig.is_combined_ref and lga50 else ''))
report = reporting.get(contigs_fpath)
report.add_field(reporting.Fields.LARGALIGN, max(lens))
report.add_field(reporting.Fields.TOTAL_ALIGNED_LEN, sum(lens))
report.add_field(reporting.Fields.NA50, na50)
report.add_field(reporting.Fields.NA75, na75)
report.add_field(reporting.Fields.LA50, la50)
report.add_field(reporting.Fields.LA75, la75)
if not qconfig.is_combined_ref:
report.add_field(reporting.Fields.NGA50, nga50)
report.add_field(reporting.Fields.NGA75, nga75)
report.add_field(reporting.Fields.LGA50, lga50)
report.add_field(reporting.Fields.LGA75, lga75)
########################################################################
num_contigs = max([len(aligned_lengths_lists[i]) for i in range(len(aligned_lengths_lists))])
if json_output_dirpath:
from quast_libs.html_saver import json_saver
json_saver.save_assembly_lengths(json_output_dirpath, aligned_contigs_fpaths, assembly_lengths)
# saving to html
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_assembly_lengths(output_dirpath, aligned_contigs_fpaths, assembly_lengths)
import plotter
if qconfig.draw_plots:
# Drawing cumulative plot (aligned contigs)...
plotter.cumulative_plot(ref_fpath, aligned_contigs_fpaths, aligned_lengths_lists,
os.path.join(aligned_stats_dirpath, 'cumulative_plot'),
'Cumulative length (aligned contigs)')
# Drawing NAx and NGAx plots...
plotter.Nx_plot(output_dirpath, num_contigs > qconfig.max_points, aligned_contigs_fpaths, aligned_lengths_lists, aligned_stats_dirpath + '/NAx_plot', 'NAx',
assembly_lengths, json_output_dir=json_output_dirpath)
if not qconfig.is_combined_ref:
plotter.Nx_plot(output_dirpath, num_contigs > qconfig.max_points, aligned_contigs_fpaths, aligned_lengths_lists,
aligned_stats_dirpath + '/NGAx_plot', 'NGAx', [reference_length for i in range(len(aligned_contigs_fpaths))], json_output_dir=json_output_dirpath)
logger.main_info('Done.')
return report_dict
def save_assembly_lengths(results_dirpath, contigs_fpaths, assemblies_lengths):
json_fpath = json_saver.save_assembly_lengths(results_dirpath, contigs_fpaths, assemblies_lengths)
if json_fpath:
append(results_dirpath, json_fpath, 'assembliesLengths')
def save_assembly_lengths(results_dirpath, contigs_fpaths, assemblies_lengths):
json_fpath = json_saver.save_assembly_lengths(results_dirpath,
contigs_fpaths,
assemblies_lengths)
if json_fpath:
append(results_dirpath, json_fpath, 'assembliesLengths')
def do(ref_fpath, aligned_contigs_fpaths, output_dirpath, json_output_dirpath,
aligned_lengths_lists, aligned_stats_dirpath):
if not os.path.isdir(aligned_stats_dirpath):
os.mkdir(aligned_stats_dirpath)
########################################################################
report_dict = {'header': []}
for contigs_fpath in aligned_contigs_fpaths:
report_dict[qutils.name_from_fpath(contigs_fpath)] = []
########################################################################
logger.print_timestamp()
logger.main_info('Running NA-NGA calculation...')
ref_chr_lengths = fastaparser.get_chr_lengths_from_fastafile(ref_fpath)
reference_length = sum(ref_chr_lengths.values())
assembly_lengths = []
for contigs_fpath in aligned_contigs_fpaths:
assembly_lengths.append(sum(fastaparser.get_chr_lengths_from_fastafile(contigs_fpath).values()))
for i, (contigs_fpath, lens, assembly_len) in enumerate(
zip(aligned_contigs_fpaths, aligned_lengths_lists, assembly_lengths)):
na50 = N50.NG50(lens, assembly_len)
na75 = N50.NG50(lens, assembly_len, 75)
la50 = N50.LG50(lens, assembly_len)
la75 = N50.LG50(lens, assembly_len, 75)
if not qconfig.is_combined_ref:
nga50 = N50.NG50(lens, reference_length)
nga75 = N50.NG50(lens, reference_length, 75)
lga50 = N50.LG50(lens, reference_length)
lga75 = N50.LG50(lens, reference_length, 75)
logger.info(' ' +
qutils.index_to_str(i) +
qutils.label_from_fpath(contigs_fpath) +
', Largest alignment = ' + str(max(lens)) +
', NA50 = ' + str(na50) +
(', NGA50 = ' + str(nga50) if not qconfig.is_combined_ref and nga50 else '') +
', LA50 = ' + str(la50) +
(', LGA50 = ' + str(lga50) if not qconfig.is_combined_ref and lga50 else ''))
report = reporting.get(contigs_fpath)
report.add_field(reporting.Fields.LARGALIGN, max(lens))
report.add_field(reporting.Fields.TOTAL_ALIGNED_LEN, sum(lens))
report.add_field(reporting.Fields.NA50, na50)
report.add_field(reporting.Fields.NA75, na75)
report.add_field(reporting.Fields.LA50, la50)
report.add_field(reporting.Fields.LA75, la75)
if not qconfig.is_combined_ref:
report.add_field(reporting.Fields.NGA50, nga50)
report.add_field(reporting.Fields.NGA75, nga75)
report.add_field(reporting.Fields.LGA50, lga50)
report.add_field(reporting.Fields.LGA75, lga75)
########################################################################
num_contigs = max([len(aligned_lengths_lists[i]) for i in range(len(aligned_lengths_lists))])
if json_output_dirpath:
from quast_libs.html_saver import json_saver
json_saver.save_assembly_lengths(json_output_dirpath, aligned_contigs_fpaths, assembly_lengths)
# saving to html
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_assembly_lengths(output_dirpath, aligned_contigs_fpaths, assembly_lengths)
if qconfig.draw_plots:
# Drawing cumulative plot (aligned contigs)...
plotter.cumulative_plot(ref_fpath, aligned_contigs_fpaths, aligned_lengths_lists,
os.path.join(aligned_stats_dirpath, 'cumulative_plot'),
'Cumulative length (aligned contigs)')
# Drawing NAx and NGAx plots...
plotter.Nx_plot(output_dirpath, num_contigs > qconfig.max_points, aligned_contigs_fpaths, aligned_lengths_lists, aligned_stats_dirpath + '/NAx_plot', 'NAx',
assembly_lengths, json_output_dir=json_output_dirpath)
if not qconfig.is_combined_ref:
plotter.Nx_plot(output_dirpath, num_contigs > qconfig.max_points, aligned_contigs_fpaths, aligned_lengths_lists,
aligned_stats_dirpath + '/NGAx_plot', 'NGAx', [reference_length for i in range(len(aligned_contigs_fpaths))], json_output_dir=json_output_dirpath)
logger.main_info('Done.')
return report_dict
