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From: Ben Keshet on 3 Jul 2008 11:02
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>ATOM" (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.
From: Bruno Desthuilliers on 3 Jul 2008 11:26
Ben Keshet a �crit :
> 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(something)

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>ATOM" (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
From: Callie Bertsche on 3 Jul 2008 14:45
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?
From: Matthew Fitzgibbons on 3 Jul 2008 15:02
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?
> --
> http://mail.python.org/mailman/listinfo/python-list
>

Leave off the beginning slash.

-Matt
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