如何用python表示交集_如何编写一个python脚本来查找两个文件之间的交集并附加原始fi...

如果两个文件都像您的例子中那样排序，那么您可以在沿着一个或两个文件智能地逐行读取时找到交叉点。这对进程的内存消耗更友好，并且不需要为file1中的每一行循环file2。对于像您的示例这样的小文件来说，这并不重要，但是当这些文件很大时，它将对您有所帮助。在

请注意，我只考虑了起始和结束列来匹配DNA链。如果其他字段也需要匹配，则此代码将不起作用(但您可以对其进行调整)。在

在现实生活中使用它之前，还需要进行更多的检查(例如，对源文件中的行进行检查)。在

代码：def read_and_parse_line(fh):

# It gets the next line,

# strip any whitespace from the end,

# split it on whitespace into fields.

return fh.next().rstrip().split()

def append_to_result(result, line):

(scaffold1, start1, end1, transcript1, type1, start2, end2, comment2) = line

# Making start and end real integers so you can work with them as such.

result.append((scaffold1, int(start1), int(end1), transcript1, type1, int(start2), int(end2), comment2))

# These will be our result lines.

result = []

# With makes sure the files are properly closed afterwards.

with open('file1') as file1, open('file2') as file2:

# Getting the iterator on the files.

file1 = iter(file1)

file2 = iter(file2)

try:

(scaffold1, start1, end1, transcript1, type1) = read_and_parse_line(file1)

read_second = True

while True:

if read_second:

try:

(scaffold2, start2, end2, comment2) = read_and_parse_line(file2)

except StopIteration:

print("File 2 ended.")

# Nothing more in the second file.

# Outputting the original line

result.append((scaffold1, start1, end1, transcript1, type1, 0, 0, None))

# Reading in a new line from the first file.

(scaffold1, start1, end1, transcript1, type1) = read_and_parse_line(file1)

if int(start1) <= int(start2):

# Second file record starts after the first file record.

if int(end1) >= int(end2):

# And the second file record ends before the first file record.

# = MATCH!!!

print("We've found a match: [%s-[%s-%s]-%s]" % (start1, start2, end2, end1))

# Write the combined line.

result.append((scaffold1, start1, end1, transcript1, type1, start2, end2, comment2))

## READ BOTH

(scaffold1, start1, end1, transcript1, type1) = read_and_parse_line(file1)

read_second = True

else:

# The second file record ends AFTER the first file record.

print("No match in second file: [%s-%s]" % (start1, end1))

# So writing out the unmodified line.

result.append((scaffold1, start1, end1, transcript1, type1, 0, 0, None))

## READ 1

(scaffold1, start1, end1, transcript1, type1) = read_and_parse_line(file1)

read_second = False

else:

# This is thrown away in your example.

print("No match in the first file for: [%s-%s]" % (start2, end2))

# Trying the next line in the second file.

read_second = True

except StopIteration:

print("File 1 ended.")

# Printing a clean line after all the logging above.

print("")

# Printing the result to screen.

# I guess you want to do more stuff with the data and not just write it to file.

for line in result:

# The 8th element being equal to None indicates there was no match.

if line[7] == None:

print("%s\t%s\t%s\t%s\t%s" % line[:5])

else:

print("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % line)