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python - 在python中将2个文本文件汇总为一个文件

问题描述

我有 2 个文件被调用big并small喜欢这些示例：

big：

chr1    transcript      2481359 2483515 -       RP3-395M20.8
chr1    transcript      2487078 2492123 +       TNFRSF14
chr1    transcript      2497849 2501297 +       RP3-395M20.7
chr1    transcript      2512999 2515942 +       RP3-395M20.9
chr1    transcript      2517930 2521041 +       FAM213B
chr1    transcript      2522078 2524087 -       MMEL1

small：

chr1    2487088 2492113 17
chr1    100757323       100757324       19
chr1    2487099 2492023 21
chr1    100758316       100758317       41
chr1    2514000 2515742 14

我尝试5 columns在以下条件下使用大文件创建一个新文件：

conditions：

1- if: the 1st column of small file == 1st column of big file
2- if: the 4th column of big file >= the 2nd column of small file >= the 3rd column of big file
3- if: the 4th column of big file >= the 3rd column of small file >= the 3rd column of big file

columns in output file：

1) 1st column of big file
2) 2nd column of big file
3) 3rd column of big file
4) the number of lines in small files that have the mentioned conditions (we should count)
5) 6th column of big file

这是上述示例的预期输出：

chr1    2487078 2492123 2       TNFRSF14
chr1    2512999 2515942 1       RP3-395M20.9

我在python. 它不会返回我想要的文件。我的代码中的每一行似乎都是合乎逻辑的。你能帮我修一下吗？

def correspond(big, small, outfile):
    count = 0
    big = open(big, "r")
    small = open(small, "r")
    big_list = []
    small_list = []
    for m in big:
        big_list.append(m)
    for n in small:
        small_list.append(n)
    final = []
    for i in range(0, len(small_list)):
        for j in range(0, len(big_list)):
            small_row = small_list[i]
            big_row = big_list[j]
            small_columns = small_row.split()
            big_columns = big_row.split()
            small_symbol = small_columns[0]
            big_symbol = big_columns[0]
            name = big_columns[5]
            if small_symbol == big_symbol:
                small_second_col = small_columns[1]
                small_third_col = small_columns[2]
                min_range = big_columns[2]
                max_range = big_columns[3]
                if (small_second_col <= max_range and small_second_col >= min_range and small_third_col <= max_range and small_third_col >= min_range):
                        count+=1
                        new_line = small_row.rstrip("\n") + " " + big_symbol + " " + min_range + " " + max_range + str(count) + name
                        final.append(new_line)
    with open(outfile, "w") as f:
        for item in final:
            f.write("%s\n" % item)

标签： python

解决方案

完整的工作解决方案，没有熊猫：

from itertools import product


def str_or_int(item):
    try:
        return int(item)
    except ValueError:
        return item

def correspond(big, small, output):
    with open(big, 'r') as bigf, open(small, 'r') as smallf, open(output, 'w') as outputf:
        current = None
        count = 0
        for b_line, s_line in product(filter(lambda x: x != '\n', bigf), filter(lambda x: x != '\n', smallf)):
            if b_line != current:
                if count > 0:
                    out_line = current.split()
                    outputf.write('\t'.join((out_line[0], out_line[1], out_line[2], str(count), out_line[5])) + '\n')
                current = b_line
                count = 0
            b_line = [str_or_int(s) for s in b_line.split()]
            s_line = [str_or_int(s) for s in s_line.split()]
            try:
                if b_line[0] == s_line[0] and b_line[3] >= s_line[1] >= b_line[2] and b_line[3] >= s_line[2] >= b_line[2]:
                    count += 1
            except IndexError:
                continue

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