Write a file - beginner's question

[Ben Keshet]

I have a probably simple beginner's question -

I have a script that I am currently able to print its output. instead,
i want to write it into a file - I tried different versions of write()
but might have gotten the syntax wrong. the variable I want to write is
a line from a file I am reading:

"...
f = open('receptor. mol2', 'r')
line = f.readline()[:-1]
while '@<TRIPOS>ATOM' not in line:
line = f.readline()[:-1]
#print line
print random_mol2
...."

e.g. I want to write to a file all the lines in 'receptor.mol2' up to
the string "@<TRIPOS>A TOM" (one after the other). Can anyone please advice?

On a related note - how do I read and write to a file that is not in the
same directory? e.g how do I provide a pathway to an open command?

Please remember that I am a very beginner in Python and programming -
Thank you.

[Bruno Desthuilliers]

Re: Write a file - beginner's question

Ben Keshet a écrit :

I have a probably simple beginner's question -
>
I have a script that I am currently able to print its output. instead,
i want to write it into a file - I tried different versions of write()
but might have gotten the syntax wrong.

The syntax is:

fileobj.write(s omething)

Now since you don't say exactly what you tried *and what you got*, we
can't help much more here.

the variable I want to write is
a line from a file I am reading:
>
"...
f = open('receptor. mol2', 'r')
line = f.readline()[:-1]

If you want to strip the newline characters, you'd better use
line.strip() or line.lstrip()

while '@<TRIPOS>ATOM' not in line:
line = f.readline()[:-1]
#print line

Also, there are simpler ways to iterate over a file:

f = open('somefile. txt')
for line in f:
if '@<TRIPOS>ATOM' in line:
break
print line.lstrip()

f.close()

print random_mol2
..."
>
e.g. I want to write to a file all the lines in 'receptor.mol2' up to
the string "@<TRIPOS>A TOM" (one after the other). Can anyone please
advice?

The simplest solution for a unix-like command-line program would be to
redirect the standard out to this file, ie:

# python myprog.py destfile.txt

But this may not fit your needs !-)


The other simplest solution is to open the destination file in write (or
append) mode and write to it:

source = open('somefile. txt')
dest = open('otherfile .txt', 'w')
for line in source:
if '@<TRIPOS>ATOM' in line:
break
# we don't strip here, since write doesn't append a newline
dest.write(line )

source.close()
dest.close()

On a related note - how do I read and write to a file that is not in the
same directory?

Give the full absolute or relative path.

e.g how do I provide a pathway to an open command?

source = open('/full/absolute/path/to/my/file.txt')

Note that the exact syntax for a path depends on your os (but the
os.path module can take care of most specificities). The above example
is for a posix system. On Windows, you'll probably have something like:

source = open('C:/full/absolute/path/to/my/file.txt')

HTH

[Callie Bertsche]

Re: Write a file - beginner's question

I have a closely related note. How do I write to a relative path with
python? Example,
source = open('/../../directory/subdirectory/file.extension' )

What am I missing?

[Matthew Fitzgibbons]

Re: Write a file - beginner's question

Callie Bertsche wrote:

I have a closely related note. How do I write to a relative path with
python? Example,
source = open('/../../directory/subdirectory/file.extension' )
>
What am I missing?
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>

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-Matt