#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import oas_file_handling as oas
import sys
from scipy.stats import chi2_contingency, chi2, spearmanr
#human_file = oas.oas_file("Vander_Heiden_2017_Heavy_HD09_IGHG_HD09_Unsorted_Bcells_age31_healthy_iglblastn_igblastn_IGHG.json.gz")
#mouse_file = oas.oas_file("Collins_2015_IGHG_Mouse_sample_2_iglblastn_igblastn_IGHG.json.gz")
#mouse_file = oas.oas_file("Corcoran_2016_heavy_mouse_IGHG_mouse_heavy_M2_igblastn_igblastn_IGHG.json.gz")
human_file = oas.oas_file(str(sys.argv[1]))
mouse_file = oas.oas_file(str(sys.argv[2]))
if len(sys.argv) > 3:
threshold = int(sys.argv[3])
else:
threshold = 1
if len(sys.argv) > 4:
significance = int(sys.argv[4])
else:
significance = 0.05
position_list = human_file.all_positions(threshold)
print("""Using data from {} and {} and a significance level of {}:
""".format(human_file.file_name, mouse_file.file_name, significance))
for position in position_list:
human_data = human_file.data_row(position)
mouse_data = mouse_file.data_row(position)
#!/usr/bin/env python3
# coding: utf-8
#%%
import sys
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import oas_file_handling as oas
f = oas.oas_file(str(sys.argv[1]))
threshold = sys.argv[2] if len(sys.argv) > 2 else 1
#f = oas_file("Vander_Heiden_2017_Heavy_HD09_IGHG_HD09_Unsorted_Bcells_age31_healthy_iglblastn_igblastn_IGHG.json.gz")
#f = oas_file("Corcoran_2016_heavy_mouse_IGHG_mouse_heavy_M2_igblastn_igblastn_IGHG.json.gz")
amino_acid_list = f.amino_acids
page = 1
for region_name in f.regions:
raw_data = {}
for amino_acid in amino_acid_list:
raw_data[amino_acid] = []
for position in f.region_positions(region_name, freq, threshold):
amino_acid_frequency = f.amino_acid_frequency(position)
if amino_acid in amino_acid_frequency:
raw_data[amino_acid].append(amino_acid_frequency[amino_acid])
else:
raw_data[amino_acid].append(0)
df = pd.DataFrame(raw_data)
import sys, math
import oas_file_handling as oas
f = oas.oas_file(
"Vander_Heiden_2017_Heavy_HD09_IGHG_HD09_Unsorted_Bcells_age31_healthy_iglblastn_igblastn_IGHG.json.gz"
)
#f = oas.oas_file("Corcoran_2016_heavy_mouse_IGHG_mouse_heavy_M2_igblastn_igblastn_IGHG.json.gz")
#f = oas.oas_file(str(sys.argv[1]))
if len(sys.argv) > 2:
threshold = int(sys.argv[2])
else:
threshold = 1
def probability(position, amino_acid):
amino_acid_frequency = f.amino_acid_frequency(position)
if amino_acid in amino_acid_frequency:
prob = amino_acid_frequency[amino_acid] / 100
else:
prob = 0
return prob
def joint_probability(position1, amino_acid1, position2, amino_acid2):
both = 0
for data in f.sequence_data:
full_sequence = f.combined_sequence(data)
if amino_acid2 == 'Unused' and position2 not in full_sequence:
if amino_acid1 == 'Unused' and position1 not in full_sequence:
both += 1
elif position1 in full_sequence and full_sequence[