def fasta_to_plot_group(fasta_file, output_dir):
lengths = []
with FastaReader(fasta_file) as f:
for record in f:
lengths.append(len(record.sequence))
from pbreports.plot.helper import get_fig_axes
from pbreports.model.model import PlotGroup, Plot
fig, ax = get_fig_axes()
if len(lengths) == 1:
v = lengths[0]
hrange = (v -1, v + 1)
ax.hist(lengths, range=hrange)
else:
ax.hist(lengths)
ax.set_title("Sequence Length Histogram")
ax.set_xlabel("Sequence Length")
name = "sequence_length_hist.png"
png_path = os.path.join(output_dir, name)
fig.savefig(png_path)
plots = [Plot("sequence_lengths", name)]
pg = PlotGroup("reference_hist", "Sequence Lengths", plots=plots)
return pg
def fasta_to_plot_group(fasta_file, output_dir):
lengths = []
with FastaReader(fasta_file) as f:
for record in f:
lengths.append(len(record.sequence))
from pbreports.plot.helper import get_fig_axes #pylint: disable=import-error
from pbcommand.models.report import PlotGroup, Plot
fig, ax = get_fig_axes()
if len(lengths) == 1:
v = lengths[0]
hrange = (v - 1, v + 1)
ax.hist(lengths, range=hrange)
else:
ax.hist(lengths)
ax.set_title("Sequence Length Histogram")
ax.set_xlabel("Sequence Length")
name = "sequence_length_hist.png"
png_path = os.path.join(output_dir, name)
fig.savefig(png_path)
plots = [Plot("sequence_lengths", name)]
pg = PlotGroup("reference_hist", "Sequence Lengths", plots=plots)
return pg
def fasta_to_plot_group(fasta_file, output_dir):
lengths = []
with FastaReader(fasta_file) as f:
for record in f:
lengths.append(len(record.sequence))
from pbreports.plot.helper import get_fig_axes
from pbreports.model.model import PlotGroup, Plot
fig, ax = get_fig_axes()
ax.hist(lengths)
ax.set_title("Sequence Length Histogram")
ax.set_xlabel("Sequence Length")
name = "sequence_length_hist.png"
png_path = os.path.join(output_dir, name)
fig.savefig(png_path)
plots = [Plot("sequence_lengths", name)]
pg = PlotGroup("reference_hist", "Sequence Lengths", plots=plots)
return pg