使用Python来减少表格形式的BLAST输出文件中的命中数

Question

我有一个表格格式的大blast文件，目标序列的数量不受限制，所以解析需要很长时间。我希望将每个查询序列的命中数减少到前10个。 我的python是基本的，但是到目前为止我所拥有的

import sys

blastfile = open(sys.argv[1],"r")

column1list=[]

for line in blastfile:
    b = line.split()[0]
    column1list.append(b)

uniqcolumn1 = list(set(column1list))

counter = 0

for val in uniqcolumn1:
    #print val
    for line in blastfile:
        #print line
        while counter <= 10:
            if line.startswith(val):
                print line
                counter =+ 1

下面是blast输出文件的一行示例，查询序列的标题在第一列中，在本例中为“c8208”g1_i2

^{pr2}$

我认为代码的第一部分工作正常，直到' uniqcolumn1=list（set（column1list））'，那么我无法让它打印以列表中每个字符串开头的前十行。在

Answer 1

此一次性版本按标题在文件中出现的顺序打印每个标题的前10个：

import sys
NUM_TO_PRINT=10     # good practice - use names rather than raw numbers

blastfile = open(sys.argv[1],"r")

titles={};  # an empty dictionary.
    # This will map titles to counts of how many times a line with that title
    # has been printed.

for line in blastfile:
    title = line.split()[0];    # assuming the title is space-delimited, and that the line is not empty
    num_printed = titles.get(title, 0);     # 0 is the default
    if num_printed<NUM_TO_PRINT:
        print line,    # comma because _line_ already has a newline - without the comma, you get a blank line after every printed line
        num_printed += 1
        titles[title] = num_printed     # save where we are