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:
from quast_libs import plotter
corr_fpaths = [asm.fpath for asm in assemblies]
corr_labels = [asm.label for asm in assemblies]
plotter.save_colors_and_ls(corr_fpaths, labels=corr_labels)
return assemblies, corrected_labels
def correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting):
## removing from contigs' names special characters because:
## 1) Some embedded tools can fail on some strings with "...", "+", "-", etc
## 2) Nucmer fails on names like "contig 1_bla_bla", "contig 2_bla_bla" (it interprets as a contig's name only the first word of caption and gets ambiguous contigs names)
if qconfig.max_threads is None:
qconfig.max_threads = 1
n_jobs = min(len(contigs_fpaths), qconfig.max_threads)
if is_python2():
from joblib import Parallel, delayed
else:
from joblib3 import Parallel, delayed
logger.main_info(' Pre-processing...')
corrected_info = Parallel(n_jobs=n_jobs)(delayed(parallel_correct_contigs)(i, contigs_fpath,
corrected_dirpath, labels) for i, contigs_fpath in enumerate(contigs_fpaths))
corrected_contigs_fpaths = []
old_contigs_fpaths = []
for contig_idx, (old_fpaths, corr_fpaths, broken_scaffold_fpaths, logs) in enumerate(corrected_info):
label = labels[contig_idx]
logger.main_info('\n'.join(logs))
for old_fpath in old_fpaths:
old_contigs_fpaths.append(old_fpath)
qconfig.assembly_labels_by_fpath[old_fpath] = label
for corr_fpath, lengths in corr_fpaths:
corrected_contigs_fpaths.append(corr_fpath)
qconfig.assembly_labels_by_fpath[corr_fpath] = label
add_lengths_to_report(lengths, reporting, corr_fpath)
for broken_fpath, lengths in broken_scaffold_fpaths:
old_contigs_fpaths.append(broken_fpath)
corrected_contigs_fpaths.append(broken_fpath)
qconfig.assembly_labels_by_fpath[broken_fpath] = label + '_broken'
add_lengths_to_report(lengths, reporting, broken_fpath)
if qconfig.draw_plots or qconfig.html_report:
from quast_libs import plotter
if not plotter.dict_color_and_ls:
plotter.save_colors_and_ls(corrected_contigs_fpaths)
return corrected_contigs_fpaths, old_contigs_fpaths
def correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting):
## removing from contigs' names special characters because:
## 1) Some embedded tools can fail on some strings with "...", "+", "-", etc
## 2) Nucmer fails on names like "contig 1_bla_bla", "contig 2_bla_bla" (it interprets as a contig's name only the first word of caption and gets ambiguous contigs names)
n_jobs = min(len(contigs_fpaths), qconfig.max_threads)
from joblib import Parallel, delayed
logger.main_info(' Pre-processing...')
corrected_info = Parallel(n_jobs=n_jobs)(
delayed(parallel_correct_contigs)(i, contigs_fpath, corrected_dirpath,
labels)
for i, contigs_fpath in enumerate(contigs_fpaths))
corrected_contigs_fpaths = []
old_contigs_fpaths = []
for contig_idx, (old_fpaths, corr_fpaths, broken_scaffold_fpaths,
logs) in enumerate(corrected_info):
label = labels[contig_idx]
logger.main_info('\n'.join(logs))
for old_fpath in old_fpaths:
old_contigs_fpaths.append(old_fpath)
qconfig.assembly_labels_by_fpath[old_fpath] = label
for corr_fpath, lengths in corr_fpaths:
corrected_contigs_fpaths.append(corr_fpath)
qconfig.assembly_labels_by_fpath[corr_fpath] = label
add_lengths_to_report(lengths, reporting, corr_fpath)
for broken_fpath, lengths in broken_scaffold_fpaths:
old_contigs_fpaths.append(broken_fpath)
corrected_contigs_fpaths.append(broken_fpath)
qconfig.assembly_labels_by_fpath[broken_fpath] = label + '_broken'
add_lengths_to_report(lengths, reporting, broken_fpath)
if qconfig.draw_plots or qconfig.html_report:
from quast_libs import plotter
if not plotter.dict_color_and_ls:
plotter.save_colors_and_ls(corrected_contigs_fpaths)
return corrected_contigs_fpaths, old_contigs_fpaths
