python 将 for 循环的输出保存到文件
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Saving output of a for-loop to file
提问by Jon
I have opened a file with blast results and printed out the hits in fasta format to the screen.
我打开了一个包含爆炸结果的文件，并将点击结果以 fasta 格式打印到屏幕上。
The code looks like this:
代码如下所示：
result_handle = open("/Users/jonbra/Desktop/my_blast.xml")
from Bio.Blast import NCBIXML
blast_records = NCBIXML.parse(result_handle)
blast_record = blast_records.next()
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
print '>', alignment.title
print hsp.sbjct
This outputs a list of fasta files to the screen. But how can I create a file and save the fasta output to this file?
这将向屏幕输出一个 fasta 文件列表。但是我怎样才能创建一个文件并将 fasta 输出保存到这个文件中呢？
Update: I guess I would have to replace the print statements within the loop with something.write(), but how will the '>', alignment.title we written?
更新：我想我必须用 something.write() 替换循环中的打印语句，但是我们写的 '>',alignment.title 将如何？
回答by truppo
First, create a file object:
首先，创建一个文件对象：
f = open("myfile.txt", "w") # Use "a" instead of "w" to append to file
You can print to a file object:
您可以打印到文件对象：
print >> f, '>', alignment.title
print >> f, hsp.sbjct
Or you can write to it:
或者你可以写信给它：
f.write('> %s\n' % (alignment.title,))
f.write('%s\n' % (hsp.sbjct,))
You can then close it to be nice:
然后你可以关闭它以示好：
f.close()
回答by John La Rooy
Something like this
像这样的东西
with open("thefile.txt","w") as f
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
f.write(">%s\n"%alignment.title)
f.write(hsp.sbjct+"\n")
prefer not to use print >>as that won't work anymore in Python3
不想使用，print >>因为这在 Python3 中不再适用
回答by Victor Kotseruba
you can use with statementto ensure that file will be closed
您可以使用with statement以确保文件将被关闭
from __future__ import with_statement
with open('/Users/jonbra/Desktop/my_blast.xml', 'w') as outfile:
from Bio.Blast import NCBIXML
blast_records = NCBIXML.parse(result_handle)
blast_record = blast_records.next()
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
outfile.write('>%s\n%s\n' % (alignment.title, hsp.sbjct))
or use try ... finally
或使用 try ... finally
outfile = open('/Users/jonbra/Desktop/my_blast.xml', 'w')
try:
from Bio.Blast import NCBIXML
blast_records = NCBIXML.parse(result_handle)
blast_record = blast_records.next()
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
outfile.write('>%s\n%s\n' % (alignment.title, hsp.sbjct))
finally:
outfile.close()
回答by Greg Hewgill
There are two general approaches. Outside of python:
有两种通用方法。在python之外：
python your_program.py >output_file.txt
Or, inside of Python:
或者，在 Python 内部：
out = open("output_file.txt", "w")
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
print >>out, '>', alignment.title
print >>out, hsp.sbjct
out.close()
回答by user3224522
for some reason the code above posted by OP did not work for me.. I modified a bit
出于某种原因，上面由 OP 发布的代码对我不起作用..我修改了一下
from Bio.Blast import NCBIXML
f = open('result.txt','w')
for record in NCBIXML.parse(open("file.xml")) :
for alignment in record.alignments:
for hsp in alignment.hsps:
f.write(">%s\n"%alignment.title)
f.write(hsp.sbjct+"\n")
