def _correct_contigs(contigs_fpaths, corrected_dirpath, min_contig, labels):
assemblies = []
for i, contigs_fpath in enumerate(contigs_fpaths):
contigs_fname = os.path.basename(contigs_fpath)
fname, ctg_fasta_ext = qutils.splitext_for_fasta_file(contigs_fname)
label = labels[i]
corr_fpath = qutils.unique_corrected_fpath(
os.path.join(corrected_dirpath, label + ctg_fasta_ext))
assembly = Assembly(corr_fpath, label)
logger.info(' %s ==> %s' % (contigs_fpath, label))
# Handle fasta
lengths = fastaparser.get_lengths_from_fastafile(contigs_fpath)
if not sum(l for l in lengths if l >= min_contig):
logger.warning(
"Skipping %s because it doesn't contain contigs >= %d bp." %
(os.path.basename(contigs_fpath), min_contig))
continue
# correcting
if not quast.correct_fasta(contigs_fpath, corr_fpath, min_contig):
continue
assemblies.append(assembly)
return assemblies
def _correct_contigs(contigs_fpaths, corrected_dirpath, min_contig, labels):
assemblies = []
for i, contigs_fpath in enumerate(contigs_fpaths):
contigs_fname = os.path.basename(contigs_fpath)
fname, ctg_fasta_ext = qutils.splitext_for_fasta_file(contigs_fname)
label = labels[i]
corr_fpath = qutils.unique_corrected_fpath(
os.path.join(corrected_dirpath, label + ctg_fasta_ext))
assembly = Assembly(corr_fpath, label)
logger.info(' %s ==> %s' % (contigs_fpath, label))
# Handle fasta
lengths = fastaparser.get_lengths_from_fastafile(contigs_fpath)
if not sum(l for l in lengths if l >= min_contig):
logger.warning("Skipping %s because it doesn't contain contigs >= %d bp."
% (os.path.basename(contigs_fpath), min_contig))
continue
# correcting
if not quast.correct_fasta(contigs_fpath, corr_fpath, min_contig):
continue
assemblies.append(assembly)
return assemblies
def _handle_fasta(contigs_fpath, corr_fpath, reporting):
lengths = fastaparser.get_lengths_from_fastafile(contigs_fpath)
if not sum(l for l in lengths if l >= qconfig.min_contig):
logger.warning(
"Skipping %s because it doesn't contain contigs >= %d bp." %
(qutils.label_from_fpath(corr_fpath), qconfig.min_contig))
return False
# correcting
if not correct_fasta(contigs_fpath, corr_fpath, qconfig.min_contig):
return False
## filling column "Assembly" with names of assemblies
report = reporting.get(corr_fpath)
## filling columns "Number of contigs >=110 bp", ">=200 bp", ">=500 bp"
report.add_field(reporting.Fields.CONTIGS__FOR_THRESHOLDS, [
sum(1 for l in lengths if l >= threshold)
for threshold in qconfig.contig_thresholds
])
report.add_field(reporting.Fields.TOTALLENS__FOR_THRESHOLDS, [
sum(l for l in lengths if l >= threshold)
for threshold in qconfig.contig_thresholds
])
return True
def fillMetrics(kind, fasta_fn):
metrics = self._metrics['spades'][kind]
lengths_all = get_lengths_from_fastafile(fasta_fn)
lengths_large = [l for l in lengths_all if l >= 500]
def i(number):
return locale.format("%d", int(number), grouping=True)
def cval(func):
return (i(func(lengths_large)), i(func(lengths_all)))
metrics['Largest ' + kind] = (i(max(lengths_all)), )
metrics['Total Length'] = cval(sum)
metrics['Number of ' + kind + 's'] = cval(len)
for q in [50, 75, 90, 95]:
metrics['N%s' % q] = cval(lambda x: N50(x, q))
def fillMetrics(kind, fasta_fn):
metrics = self._metrics['spades'][kind]
lengths_all = get_lengths_from_fastafile(fasta_fn)
lengths_large = [l for l in lengths_all if l >= 500]
def i(number):
return locale.format("%d", int(number), grouping=True)
def cval(func):
return (i(func(lengths_large)), i(func(lengths_all)))
metrics['Largest ' + kind] = (i(max(lengths_all)), )
metrics['Total Length'] = cval(sum)
metrics['Number of ' + kind + 's'] = cval(len)
for q in [50, 75, 90, 95]:
metrics['N%s' % q] = cval(lambda x: N50(x, q))
def _handle_fasta(contigs_fpath, corr_fpath, reporting):
lengths = fastaparser.get_lengths_from_fastafile(contigs_fpath)
if not sum(l for l in lengths if l >= qconfig.min_contig):
logger.warning("Skipping %s because it doesn't contain contigs >= %d bp."
% (qutils.label_from_fpath(corr_fpath), qconfig.min_contig))
return False
# correcting
if not correct_fasta(contigs_fpath, corr_fpath, qconfig.min_contig):
return False
## filling column "Assembly" with names of assemblies
report = reporting.get(corr_fpath)
## filling columns "Number of contigs >=110 bp", ">=200 bp", ">=500 bp"
report.add_field(reporting.Fields.CONTIGS__FOR_THRESHOLDS,
[sum(1 for l in lengths if l >= threshold)
for threshold in qconfig.contig_thresholds])
report.add_field(reporting.Fields.TOTALLENS__FOR_THRESHOLDS,
[sum(l for l in lengths if l >= threshold)
for threshold in qconfig.contig_thresholds])
return True
def cumulative_plot(reference, contigs_fpaths, lists_of_lengths, plot_fpath, title):
if matplotlib_error:
return
logger.info(' Drawing cumulative plot...')
import matplotlib.pyplot
import matplotlib.ticker
figure = matplotlib.pyplot.figure()
matplotlib.pyplot.rc('font', **font)
max_x = 0
max_y = 0
color_id = 0
for (contigs_fpath, lenghts) in itertools.izip(contigs_fpaths, lists_of_lengths):
lenghts.sort(reverse=True)
# calculate values for the plot
vals_contig_index = [0]
vals_length = [0]
lcur = 0
lind = 0
for l in lenghts:
lcur += l
lind += 1
x = lind
vals_contig_index.append(x)
y = lcur
vals_length.append(y)
# add to plot
if len(vals_contig_index) > 0:
max_x = max(vals_contig_index[-1], max_x)
max_y = max(max_y, vals_length[-1])
color, ls, color_id = get_color_and_ls(color_id, contigs_fpath)
matplotlib.pyplot.plot(vals_contig_index, vals_length, color=color, lw=line_width, ls=ls)
if reference:
reference_length = sum(fastaparser.get_lengths_from_fastafile(reference))
matplotlib.pyplot.plot([0, max_x], [reference_length, reference_length],
color=reference_color, lw=line_width, ls=reference_ls)
max_y = max(max_y, reference_length)
if with_title:
matplotlib.pyplot.title(title)
matplotlib.pyplot.grid(with_grid)
ax = matplotlib.pyplot.gca()
# Shink current axis's height by 20% on the bottom
box = ax.get_position()
ax.set_position([box.x0, box.y0 + box.height * 0.2, box.width, box.height * 0.8])
legend_list = map(qutils.label_from_fpath, contigs_fpaths)
if reference:
legend_list += ['Reference']
# Put a legend below current axis
try: # for matplotlib <= 2009-12-09
ax.legend(legend_list, loc='upper center', bbox_to_anchor=(0.5, -0.1), fancybox=True,
shadow=True, ncol=n_columns)
except Exception: # ZeroDivisionError: ValueError:
pass
ylabel = 'Cumulative length '
ylabel, mkfunc = y_formatter(ylabel, max_y)
matplotlib.pyplot.xlabel('Contig index', fontsize=axes_fontsize)
matplotlib.pyplot.ylabel(ylabel, fontsize=axes_fontsize)
mkformatter = matplotlib.ticker.FuncFormatter(mkfunc)
ax.yaxis.set_major_formatter(mkformatter)
xLocator, yLocator = get_locators()
ax.yaxis.set_major_locator(yLocator)
ax.xaxis.set_major_locator(xLocator)
#ax.set_yscale('log')
#matplotlib.pyplot.ylim([0, int(float(max_y) * 1.1)])
plot_fpath += plots_file_ext
matplotlib.pyplot.savefig(plot_fpath)
logger.info(' saved to ' + plot_fpath)
pdf_plots_figures.append(figure)
def cumulative_plot(reference, contigs_fpaths, lists_of_lengths, plot_fpath, title):
if matplotlib_error:
return
logger.info(' Drawing cumulative plot...')
import matplotlib.pyplot
import matplotlib.ticker
figure = matplotlib.pyplot.figure()
matplotlib.pyplot.rc('font', **font)
max_x = 0
max_y = 0
for (contigs_fpath, lenghts) in itertools.izip(contigs_fpaths, lists_of_lengths):
vals_length = [0]
for l in sorted(lenghts, reverse=True):
vals_length.append(vals_length[-1] + l)
vals_contig_index = range(0, len(vals_length))
if vals_contig_index:
max_x = max(vals_contig_index[-1], max_x)
max_y = max(max_y, vals_length[-1])
color, ls = get_color_and_ls(contigs_fpath)
matplotlib.pyplot.plot(vals_contig_index, vals_length, color=color, lw=line_width, ls=ls)
if reference:
y_vals = []
for l in sorted(fastaparser.get_lengths_from_fastafile(reference), reverse=True):
if y_vals:
y_vals.append(y_vals[-1] + l)
else:
y_vals = [l]
x_vals = range(1, len(y_vals) + 1) # for reference only: starting from X=1
# extend reference curve to the max X-axis point
reference_length = y_vals[-1]
max_x = max(max_x, x_vals[-1])
max_y = max(max_y, reference_length)
y_vals.append(reference_length)
x_vals.append(max_x)
matplotlib.pyplot.plot(x_vals, y_vals,
color=reference_color, lw=line_width, ls=reference_ls)
if with_title:
matplotlib.pyplot.title(title)
matplotlib.pyplot.grid(with_grid)
ax = matplotlib.pyplot.gca()
# Shink current axis's height by 20% on the bottom
box = ax.get_position()
ax.set_position([box.x0, box.y0 + box.height * 0.2, box.width, box.height * 0.8])
legend_list = map(qutils.label_from_fpath, contigs_fpaths)
if reference:
legend_list += ['Reference']
# Put a legend below current axis
try: # for matplotlib <= 2009-12-09
ax.legend(legend_list, loc='upper center', bbox_to_anchor=(0.5, -0.1), fancybox=True,
shadow=True, ncol=n_columns if n_columns<3 else 3)
except Exception: # ZeroDivisionError: ValueError:
pass
ylabel = 'Cumulative length '
ylabel, mkfunc = y_formatter(ylabel, max_y)
matplotlib.pyplot.xlabel('Contig index', fontsize=axes_fontsize)
matplotlib.pyplot.ylabel(ylabel, fontsize=axes_fontsize)
mkformatter = matplotlib.ticker.FuncFormatter(mkfunc)
ax.yaxis.set_major_formatter(mkformatter)
xLocator, yLocator = get_locators()
ax.yaxis.set_major_locator(yLocator)
ax.xaxis.set_major_locator(xLocator)
if logarithmic_x_scale:
ax.set_xscale('log')
#ax.set_yscale('log')
#matplotlib.pyplot.ylim([0, int(float(max_y) * 1.1)])
plot_fpath += plots_file_ext
matplotlib.pyplot.savefig(plot_fpath, bbox_inches='tight')
logger.info(' saved to ' + plot_fpath)
pdf_plots_figures.append(figure)