default=None,
help="Title of figure. Default: not set")
parser.add_argument(
"-m",
"--parsing_mode",
action="store",
dest="parsing_mode",
default="genotypes",
help=
"Parsing mode. Allowed: genotypes(default), 'coordinates_and_genotypes', 'complete'"
)
"""
parser.add_argument("-a", "--scaffold_white_list", action="store", dest="scaffold_white_list", default=[],
type=lambda s: s.split(","),
help="Comma-separated list of the only scaffolds to draw. Default: all")
parser.add_argument("-b", "--scaffold_black_list", action="store", dest="scaffold_black_list", default=[],
type=lambda s: s.split(","),
help="Comma-separated list of scaffolds to skip at drawing. Default: not set")
"""
args = parser.parse_args()
mutations = CollectionVCF(args.input, parsing_mode="genotypes")
StatsVCF.count_singletons(collection_vcf=mutations,
output_prefix=args.output_prefix)
"""
Visualization.zygoty_bar_plot(StatsVCF.count_zygoty(mutations, outfile="%s.counts" % args.output_prefix),
args.output_prefix, extension_list=args.output_formats,
figsize=args.figsize,
dpi=args.dpi,
title=args.title)
"""
extracting_method=args.method,
threshold_tuple=None,
min_threshold=args.min_threshold,
max_threshold=args.max_threshold,
threshold_number=None,
threshold_step=args.threshold_step,
output_prefix=None)
"""
output_prefix = "%s.D%s.M%s.depth%i" % (args.output_prefix, args.distance,
args.method, args.depth)
cluster_df = StatsVCF.test_clustering_thresholds(
variants.records,
method=args.distance,
output_prefix=output_prefix,
extracting_method=args.method,
threshold_tuple=None,
depth=args.depth,
min_threshold=args.min_threshold,
max_threshold=args.max_threshold,
threshold_number=None,
threshold_step=args.threshold_step,
)
print("Drawing...")
Visualization.plot_clustering_threshold_tests(
cluster_df,
output_prefix,
scaffold_order_list=args.scaffold_ordered_list,
extensions=("png", ),
suptitle="Test of clustering thresholds")
print(scaffold_to_keep)
print(coverage_df)
print(chr_syn_dict)
print(coverage_df)
Visualization.draw_coverage_windows(
coverage_df,
args.window_size,
args.window_step,
chr_len_df,
average_coverage_dict,
args.output_prefix,
figure_width=args.figure_width,
figure_height_per_scaffold=args.figure_height_per_scaffold,
dpi=300,
colormap=args.colormap,
title=args.title,
extensions=args.output_formats,
scaffold_order_list=args.scaffold_ordered_list,
test_colormaps=args.test_colormaps,
thresholds=(0.0, 0.125, 0.25, 0.375, 0.5, 0.625, 0.75, 0.875, 1.0, 1.125,
1.25, 1.375, 1.5, 1.625, 1.75, 1.875, 2.0, 2.125, 2.25)
if args.split_coverage_thresholds else args.coverage_thresholds,
absolute_coverage_values=args.absolute_coverage_values,
subplots_adjust_left=args.subplots_adjust_left,
subplots_adjust_bottom=args.subplots_adjust_bottom,
subplots_adjust_right=args.subplots_adjust_right,
subplots_adjust_top=args.subplots_adjust_top,
show_track_label=not args.hide_track_label,
show_trackgroup_label=True)
type=lambda s: map(int, s.split(",")),
default=(5, 5),
help="Size of figure in inches. X and Y values should be separated "
"by comma. Default: 5,5")
parser.add_argument("-e", "--output_formats", action="store", dest="output_formats",
type=lambda s: s.split(","),
default=["png"],
help="Comma-separated list of formats (supported by matlotlib) "
"of output figure.Default: png")
parser.add_argument("-l", "--title", action="store", dest="title",
default=None,
help="Title of figure. Default: not set")
"""
parser.add_argument("-a", "--scaffold_white_list", action="store", dest="scaffold_white_list", default=[],
type=lambda s: s.split(","),
help="Comma-separated list of the only scaffolds to draw. Default: all")
parser.add_argument("-b", "--scaffold_black_list", action="store", dest="scaffold_black_list", default=[],
type=lambda s: s.split(","),
help="Comma-separated list of scaffolds to skip at drawing. Default: not set")
"""
args = parser.parse_args()
mutations = CollectionVCF(args.input, parsing_mode="coordinates_and_genotypes")
Visualization.zygoty_bar_plot(StatsVCF.count_zygoty(mutations, outfile="%s.counts" % args.output_prefix),
args.output_prefix, extension_list=args.output_formats,
figsize=args.figsize,
dpi=args.dpi,
title=args.title)
#print(masking_df)
#print(count_df)
count_df.to_csv("%s.variant_counts.with_masking.tsv" %
args.output_prefix,
sep='\t',
header=True,
index=True)
Visualization.draw_variant_window_densities(
count_df,
args.window_size,
args.window_step,
chr_len_df,
args.output_prefix,
figure_width=15,
figure_height_per_scaffold=0.5,
dpi=300,
show_track_label=not args.hide_track_label,
colormap=args.colormap,
title=args.title,
extensions=args.output_formats,
scaffold_order_list=args.scaffold_ordered_list,
test_colormaps=args.test_colormaps,
thresholds=args.density_thresholds,
masking=True if args.coverage else False,
subplots_adjust_left=args.subplots_adjust_left,
subplots_adjust_bottom=args.subplots_adjust_bottom,
subplots_adjust_right=args.subplots_adjust_right,
subplots_adjust_top=args.subplots_adjust_top,
show_trackgroup_label=True)
#print(chr_len_df)
Visualization.draw_features(feature_df,
chr_len_df,
args.output_prefix,
legend_df=legend_df,
figure_width=15,
figure_height_per_scaffold=0.5,
dpi=300,
colormap=None,
thresholds=None,
colors=None,
background=None,
default_color=args.default_color,
title=None,
extensions=args.output_formats,
scaffold_order_list=args.scaffold_ordered_list,
feature_shape=args.feature_shape,
feature_start_column_id=feature_start_column_id,
feature_end_column_id=feature_end_column_id,
feature_color_column_id=args.color_column_name,
feature_length_column_id="length",
subplots_adjust_left=args.subplots_adjust_left,
subplots_adjust_bottom=args.subplots_adjust_bottom,
subplots_adjust_right=args.subplots_adjust_right,
subplots_adjust_top=args.subplots_adjust_top,
show_track_label=not args.hide_track_label,
show_trackgroup_label=True,
subplot_scale=args.subplot_scale,
track_group_scale=args.track_group_scale)
#print(label)
scaf_df_list[-1].rename(index={scaf: label}, inplace=True)
len_dict[label] = chr_len_df.loc[scaf]
len_df = pd.DataFrame.from_dict(len_dict, orient="index")
#print(len_df)
#merged_coverage_df_dict[scaf] = pd.concat(scaf_df_list)
#print(scaf)
Visualization.draw_coverage_windows(pd.concat(scaf_df_list),
args.window_size, args.window_step, len_df,
mean_coverage_df,
"{0}.{1}".format(args.output_prefix, scaf),
figure_width=args.figure_width,
figure_height_per_scaffold=args.figure_height_per_scaffold, dpi=300,
colormap=args.colormap, title="Coverage {0}".format(scaf),
extensions=args.output_formats,
scaffold_order_list=args.scaffold_ordered_list,
test_colormaps=args.test_colormaps,
thresholds=args.coverage_thresholds,
absolute_coverage_values=args.absolute_coverage_values,
subplots_adjust_left=args.subplots_adjust_left,
subplots_adjust_bottom=args.subplots_adjust_bottom,
subplots_adjust_right=args.subplots_adjust_right,
subplots_adjust_top=args.subplots_adjust_top,
show_track_label=True,
show_trackgroup_label=True,
close_figure=True
)