如何在python中逐行并行读取两个文件? [英] How to read two files in parallel, line by line, in python?
问题描述
我一直在努力解决这一问题，但没有成功.
I've been trying to solve this issue all day without success.
我有一个原始文件"，我们称它为"infile"，这是我要编辑的文件. 另外，我还有另一个充当字典"的文件，我们称它为"inlist".
I have an 'original file', let's call it 'infile', which is the file I want to edit. Additionaly I have another file that functions as a 'dictionary', let's call it 'inlist'.
以下是infile的示例:
Here are examples of the infile:
PRMT6 10505 Q96LA8 HMGA1 02829 NP_665906
WDR77 14387 NP_077007 SNRPE 00548 NP_003085
NCOA3 03570 NP_858045 RELA 01241 NP_068810
ITCH 07565 Q96J02 DTX1 03991 NP_004407
还有inlist:
NP_060607 Q96LA8
NP_001244066 Q96J02
NP_077007 Q9BQA1
NP_858045 Q9Y6Q9
我当前的方法是在相应的列中拆分行，并通过现有的选项卡拆分行. 目的是读取infile的每一行并检查一些内容:
My current approach consists in splitting the lines in the respective columns, splitting the lines by the existing tabs. The objective is to read each line of the infile and check some stuff:
- 如果在inlist的第一列中找到了infile的第三列中的元素，请将该元素更改为inlist的第二列中的相应元素
- 如果在inlist的第二列中找到了infile的第三列中的元素，则不执行任何操作
- 与infile的第5列相同
这应该检索输出:
PRMT6 10505 Q96LA8 HMGA1 02829 Q(...)
WDR77 14387 Q9BQA1 SNRPE 00548 Q(...)
NCOA3 03570 Q9Y6Q9 RELA 01241 Q(...)
ITCH 07565 Q96J02 DTX1 03991 Q(...)
注意:并非所有代码都以Q开头
NOTE: not all codes start with Q
我曾经尝试过使用while循环，但没有成功，我很ham愧将代码发布到这里(我是编程新手，所以我不想这么早就被游戏'). 完美解决此问题的方法是:
I've tried using a while loop, but wasn't successful and I'm to ashamed to post the code here (I'm new to programming, so I don't want to get demotivated so early in the 'game'). Something that would be perfect to solve this would be:
for line in inlist #, infile: <--- THIS PART! Reading both files, splitting both files, replacing both files...
inlistcolumns = line.split('\t')
infilecolumns = line.split('\t')
if inlistcolumns[0] in infilecolumns[2]:
outfile.write(str(infilecolumns[0]) + "\t" + str(infilecolumns[1]) + "\t" + str(inlistcolumns[1]) + "\t" + str(infilecolumns[3]) + "\t" + str(infilecolumns[4]) + "\t" + str(infilecolumns[5]) + "\n")
elif inlistcolumns[0] in infilecolumns[5]:
outfile.write(str(infilecolumns[0]) + "\t" + str(infilecolumns[1]) + "\t" + str(infilecolumns[2]) + "\t" + str(infilecolumns[3]) + "\t" + str(infilecolumns[4]) + "\t" + str(inlistcolumns[1]) + "\n")
else:
outfile.write('\t'.join(infilecolumns) + '\n')
我们将不胜感激.谢谢！
Help would be much appreciated. Thanks!
好吧，在Sephallia和Jlengrand的提示下，我得到了:
Ok, after the hints of Sephallia and Jlengrand I got this:
for line in infile:
try:
# Read lines in the dictionary
line2 = inlist.readline()
inlistcolumns = line.split('\t')
infilecolumns = line.split('\t')
if inlistcolumns[0] in infilecolumns[2]:
outfile.write(str(infilecolumns[0]) + "\t" + str(infilecolumns[1]) + "\t" + str(inlistcolumns[1]) + "\t" + str(infilecolumns[3]) + "\t" + str(infilecolumns[4]) + "\t" + str(infilecolumns[5]))
elif inlistcolumns[0] in infilecolumns[5]:
outfile.write(str(infilecolumns[0]) + "\t" + str(infilecolumns[1]) + "\t" + str(infilecolumns[2]) + "\t" + str(infilecolumns[3]) + "\t" + str(infilecolumns[4]) + "\t" + str(inlistcolumns[1]))
else:
outfile.write('\t'.join(infilecolumns))
except IndexError:
print "End of dictionary reached. Restarting from top."
问题在于，显然if语句没有完成其工作，因为输出文件仍然等于输入文件.我该怎么办?
The problem is that apparently the if statements are not doing their job, as the output file remained equal to the input file. What can I be doing wrong?
有些人问，这里是完整的代码:
As asked by some, here goes the full code:
import os
def replace(infilename, linename, outfilename):
# Open original file and output file
infile = open(infilename, 'rt')
inlist = open(linename, 'rt')
outfile = open(outfilename, 'wt')
# Read lines and find those to be replaced
for line in infile:
infilecolumns = line.split('\t')
line2 = inlist.readline()
inlistcolumns = line2.split('\t')
if inlistcolumns[0] in infilecolumns[2]:
outfile.write(str(infilecolumns[0]) + "\t" + str(infilecolumns[1]) + "\t" + str(inlistcolumns[1]) + "\t" + str(infilecolumns[3]) + "\t" + str(infilecolumns[4]) + "\t" + str(infilecolumns[5]))
elif inlistcolumns[0] in infilecolumns[5]:
outfile.write(str(infilecolumns[0]) + "\t" + str(infilecolumns[1]) + "\t" + str(infilecolumns[2]) + "\t" + str(infilecolumns[3]) + "\t" + str(infilecolumns[4]) + "\t" + str(inlistcolumns[1]))
outfile.write('\t'.join(infilecolumns))
# Close files
infile.close()
inlist.close()
outfile.close()
if __name__ == '__main__':
wdir = os.getcwd()
outdir = os.path.join(wdir, 'results.txt')
outname = os.path.basename(outdir)
original = raw_input("Type the name of the file to be parsed\n")
inputlist = raw_input("Type the name of the libary to be used\n")
linesdir = os.path.join(wdir, inputlist)
linesname = os.path.basename(linesdir)
indir = os.path.join(wdir, original)
inname = os.path.basename(indir)
replace(indir, linesdir, outdir)
print "Successfully applied changes.\nOriginal: %s\nLibrary: %s\nOutput:%s" % (inname, linesname, outname)
要使用的第一个文件是hprdtotal.txt: https://www.dropbox .com/s/hohvlcdqvziewte/hprdmap.txt 第二个是hprdmap.txt: https://www.dropbox.com/s/9hd0e3a8rt95pao /hprdtotal.txt
The first file to be used is hprdtotal.txt: https://www.dropbox.com/s/hohvlcdqvziewte/hprdmap.txt And the second is hprdmap.txt: https://www.dropbox.com/s/9hd0e3a8rt95pao/hprdtotal.txt
希望这会有所帮助.
推荐答案
好，我发现了. 这就是我所做的:
Ok, I found it out. This is what I did:
data = {}
for line in inlist:
k, v = [x.strip() for x in line.split('\t')]
data[k] = v
for line in infile:
infilecolumns = line.strip().split('\t')
value1 = data.get(infilecolumns[2])
value2 = data.get(infilecolumns[5])
if value1:
infilecolumns[2] = value1
if value2:
infilecolumns[5] = value2
outfile.write('\t'.join(infilecolumns) + '\n')
这给所需的输出带来了轻松愉快的体验. 感谢您的所有回答，对我有很大帮助！
This gives the desired output nice and easy. Thanks for all your answers, helped me a lot!
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