在python中将2个文本文件汇总为一个文件

Question

我有 2 个文件被调用big并small喜欢这些示例：big：chr1    transcript      2481359 2483515 -       RP3-395M20.8chr1    transcript      2487078 2492123 +       TNFRSF14chr1    transcript      2497849 2501297 +       RP3-395M20.7chr1    transcript      2512999 2515942 +       RP3-395M20.9chr1    transcript      2517930 2521041 +       FAM213Bchr1    transcript      2522078 2524087 -       MMEL1small：chr1    2487088 2492113 17chr1    100757323       100757324       19chr1    2487099 2492023 21chr1    100758316       100758317       41chr1    2514000 2515742 14我试图5 columns在以下条件下从大文件创建一个新文件：conditions ：1- if: the 1st column of small file == 1st column of big file2- if: the 4th column of big file >= the 2nd column of small file >= the 3rd column of big file3- if: the 4th column of big file >= the 3rd column of small file >= the 3rd column of big filecolumns in output file：1) 1st column of big file2) 2nd column of big file3) 3rd column of big file4) 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       TNFRSF14chr1    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 = []

Answer 1

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

如果您有问题，请在评论中提问

Answer 2

鉴于您的示例输入是这样的：

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'''

big, small = ([l.split() for l in d.splitlines()] for d in (big, small))

您可以使用sum生成器表达式来计算small符合条件的行数，然后用于str.join生成所需的输出：

for name_big, _, low, high, _, note in big:

    count = sum(1 for name_small, n1, n2, _ in small if name_big == name_small and all(int(low) <= int(n) <= int(high) for n in (n1, n2)))

    if count:

        print('\t'.join((name_big, low, high, str(count), note)))

这输出：

chr1    2487078 2492123 2   TNFRSF14

chr1    2512999 2515942 1   RP3-395M20.9