diff --git a/figures/composite_fig_5.py b/figures/composite_fig_5.py index b9f7507..25734b0 100755 --- a/figures/composite_fig_5.py +++ b/figures/composite_fig_5.py @@ -1,8 +1,7 @@ #!/usr/bin/env python3 -from pathlib import Path import sys - +from pathlib import Path sys.path.append("..") diff --git a/figures/composite_fig_6.py b/figures/composite_fig_6.py index a390d92..f203c81 100755 --- a/figures/composite_fig_6.py +++ b/figures/composite_fig_6.py @@ -4,9 +4,9 @@ from dataclasses import dataclass import matplotlib.pyplot as plt # type: ignore +import numpy as np from matplotlib.lines import Line2D # type: ignore from scipy.stats import gmean -import numpy as np PERCENTILES = [5, 25, 50, 75, 95] diff --git a/preprint_stats/cost_required_stat.py b/preprint_stats/cost_required_stat.py index c76905a..3ee006f 100755 --- a/preprint_stats/cost_required_stat.py +++ b/preprint_stats/cost_required_stat.py @@ -2,8 +2,9 @@ import csv from dataclasses import dataclass -from scipy.stats import gmean + import numpy as np +from scipy.stats import gmean PERCENTILES = [5, 25, 50, 75, 95] diff --git a/preprint_stats/family_percentage_stat.py b/preprint_stats/family_percentage_stat.py index 68a12db..a667afc 100644 --- a/preprint_stats/family_percentage_stat.py +++ b/preprint_stats/family_percentage_stat.py @@ -1,17 +1,16 @@ -import os import gzip import json +import os import subprocess + import matplotlib.pyplot as plt # type: ignore -from matplotlib.gridspec import GridSpec import matplotlib.ticker as ticker - -import pandas as pd -from scipy.stats import gmean import numpy as np -from PIL import Image +import pandas as pd import seaborn as sns - +from matplotlib.gridspec import GridSpec +from PIL import Image +from scipy.stats import gmean dashboard = os.path.expanduser("~/code/mgs-pipeline/dashboard/") diff --git a/preprint_stats/preprint_stats.py b/preprint_stats/preprint_stats.py index fa6891b..ac6569c 100644 --- a/preprint_stats/preprint_stats.py +++ b/preprint_stats/preprint_stats.py @@ -1,10 +1,10 @@ -import os import json +import os import subprocess + import numpy as np from scipy.stats import gmean - dashboard = os.path.expanduser("~/code/mgs-pipeline/dashboard/") with open(os.path.join(dashboard, "human_virus_sample_counts.json")) as inf: diff --git a/preprint_stats/reads_required_stat.py b/preprint_stats/reads_required_stat.py index ad3b652..c466750 100755 --- a/preprint_stats/reads_required_stat.py +++ b/preprint_stats/reads_required_stat.py @@ -2,9 +2,9 @@ import csv from dataclasses import dataclass -from scipy.stats import gmean import numpy as np +from scipy.stats import gmean PERCENTILES = [5, 25, 50, 75, 95] diff --git a/preprint_stats/rothman_inter_site_comparison.py b/preprint_stats/rothman_inter_site_comparison.py index 80aea4b..4de63c7 100644 --- a/preprint_stats/rothman_inter_site_comparison.py +++ b/preprint_stats/rothman_inter_site_comparison.py @@ -1,8 +1,9 @@ import csv +from collections import defaultdict +from math import log + import pandas as pd from scipy.stats import gmean -from math import log -from collections import defaultdict PERCENTILES = ["5%", "25%", "50%", "75%", "95%"] diff --git a/preprint_stats/spurbeck_inter_site_comparison.py b/preprint_stats/spurbeck_inter_site_comparison.py index 3e3ab04..9617206 100644 --- a/preprint_stats/spurbeck_inter_site_comparison.py +++ b/preprint_stats/spurbeck_inter_site_comparison.py @@ -1,8 +1,9 @@ import csv +from collections import defaultdict +from math import log + import pandas as pd from scipy.stats import gmean -from math import log -from collections import defaultdict PERCENTILES = ["5%", "25%", "50%", "75%", "95%"]