HiCAT

[duhuipeng]

Dear author Could you share the code of these two pictures？ Best HuipengDu

[yangxiaofeill]

Hi Huipeing, The dotplot is generated by Gepard [https://github.com/univieCUBE/gepard] The barplot is plotted by python, and the code is

file = 'out_hor.normal.fa' # input HOR fa
target_pattern = 'R3L6'
outfile = target_pattern+'.pdf' # outfile

dis_table = {}
rHORs = set()

rHORs_table = {}
with open(file,'r') as f:
    while True:
        line = f.readline()[:-1]
        if not line:
            break
        header = line
        seq = f.readline()[:-1]
        items = header.split(' ')
        pattern = items[0].split('::')[0][1:]
        if pattern != target_pattern:
            continue
        anno = items[1].split('::')
        rHor = anno[1][5:].split('_')
        if len(rHor) not in dis_table.keys():
            dis_table[len(rHor)] = 1
        else:
            dis_table[len(rHor)] += 1
        # print(header)
        for i in rHor:
            if i not in rHORs_table.keys():
                rHORs_table[i] = 1
            else:
                rHORs_table[i] += 1
mindis = sorted(list(dis_table.keys()))

final_dis_table = {}
for i in mindis:
    if i < 30:
        final_dis_table[i] = dis_table[i]
    else:
        if 30 not in final_dis_table.keys():
            final_dis_table[30] = dis_table[i]
        else:
            final_dis_table[30] += dis_table[i]
print(final_dis_table) # bar values
mindis = sorted(list(final_dis_table.keys()))
x = range(len(mindis))
y = []
tick_label = []
for i in mindis:
    y.append(final_dis_table[i])
    tick_label.append(i)

import numpy as np
import matplotlib.pyplot as plt
bar_width = 0.3
plt.figure(figsize=(10,8))
plt.bar(x, y, tick_label=tick_label, width=bar_width)
plt.savefig(outfile)
plt.close()

[duhuipeng]

Dear author What is the code command？ I'm under this out_hor.normal.fa file Why my command line generation doesn't generate results My code is as follows： python3 barplot.py my result as follow:

[duhuipeng]

Dear author What are the parameters you set for your word and window using gepard? Best HuipengDu

[duhuipeng]

Dear author If I can clearly see the regular HOR, shall I set word and window as the length of HOR？ How do I set these parameters if there is no apparent regularity of HOR？ This is my result under different Windows，How should an indicator selection be made to determine which one is more suitable

Best HuipengDu