Orthofinder產(chǎn)生的Orthogroups.GeneCount.tsv不能直接作為CAFE軟件的輸入文件，需要做如下處理：
filter_large_gene_family.py

#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
    作者：徐詩芬
    內(nèi)容：1.cafe的輸入格式：去掉total這一列,在第一列添加Description，然后這一列都為空
         2.過濾掉一個或多個物種有超過200個基因拷貝的基因家族，size=200
    日期：2021.2.3
"""
import sys
from itertools import islice

def usage():
    print('Usage: python filter_large_gene_family.py [index_file] [size]')


def main():
    ouf1 = open("cafe_gene_family_format.txt", 'wt')
    ouf2 = open("cafe_large_gene_family_format.txt", 'wt')

    size = eval(sys.argv[2])
    with open(sys.argv[1], 'rt') as f:
        for head in islice(f, 0, 1):  #提取第一行內(nèi)容
            head = head.strip().split("\t")[:-1]
            ouf1.write("Description\t")
            ouf2.write("Description\t")
            for h in head:
                ouf1.write(h + "\t")
                ouf2.write(h + "\t")
            ouf1.write("\n")
            ouf2.write("\n")
        for line in islice(f, 0, None):  # 跳過第一行按行讀取文件內(nèi)容
            gene_count = line.strip().split("\t")[:-1]
            family_name = gene_count[0]
            gene_list = list(map(int, gene_count[1:]))
            x = [i for i in gene_list if i > size]  # 從列表中找出大于某個值的元素
            if len(x) > 0:
                ouf2.write("\t")
                for n in gene_count:
                    ouf2.write(n)
                    ouf2.write("\t")
                ouf2.write("\n")
            else:
                ouf1.write("\t")
                for n in gene_count:
                    ouf1.write(n)
                    ouf1.write("\t")
                ouf1.write("\n")



    ouf1.close()
    ouf2.close()


try:
    main()
except IndexError:
    usage()