Re: 'While' question

[Ben Keshet]

Thanks. I tried to use 'for' instead of 'while' as both of you
suggested. It's running well as my previous version but breaks
completely instead of just skipping the empty file. I suspect the
reason is that this part is inside another 'for' so it stops
everything. I just want to it to break only one 'for', that is go back
to 5th line in the example code (directory C has one empty file):

receptors = ['A', 'B', 'C']
for x in receptors:
print x
for i in range(3):
for r in (7, 9, 11, 13, 15, 17):
f =
open('c:/Linux/Dock_method_validation/%s/validation/ligand_ran_line_%s_%sA_secondary_scored.mol2'
%(x,i,r), 'r')
line = f.readline()[:-1]
out_file =
open('c:/Linux/Dock_method_validation/%s/validation/pockets.out' %(x),'a')
out_file.write('%s ' %i)
out_file.write('%s ' %r)
# skip to scores
j=0
for line in f:
line = line.rstrip()
if "PRIMARY" not in line:
j += 1
if j == 20:
break
else:
for line in f:
if "TRIPOS" not in line:
line = line.rstrip()
out_file.write(line)
else:
break
f.close()
out_file.close()

Any suggestions as for how to control the "extent of break"? should I do
something else instead? Thank you!

[Wojtek Walczak]

On Fri, 22 Aug 2008 10:42:13 -0400, Ben Keshet wrote:

Thanks. I tried to use 'for' instead of 'while' as both of you
suggested. It's running well as my previous version but breaks
completely instead of just skipping the empty file. I suspect the
reason is that this part is inside another 'for' so it stops
everything. I just want to it to break only one 'for', that is go back
to 5th line in the example code (directory C has one empty file):

for line in f:

^^^

line = line.rstrip()
if "PRIMARY" not in line:
j += 1
if j == 20:
break
else:
for line in f:

^^^
You're iterating through the same value in inner and outer loop.
Don't do that. It's hard to predict the behavior of such a code.

Regarding break statement, it breaks only the inner loop
and returns to the outer loop/block.

It would be great if you could reduce your code to a short piece
that illustrates your problem and that we could all run.

--
Regards,
Wojtek Walczak,
http://tosh.pl/gminick/

[Ben Keshet]

Wojtek Walczak wrote:

On Fri, 22 Aug 2008 10:42:13 -0400, Ben Keshet wrote:

>Thanks. I tried to use 'for' instead of 'while' as both of you
suggested. It's running well as my previous version but breaks
completely instead of just skipping the empty file. I suspect the
reason is that this part is inside another 'for' so it stops
everything. I just want to it to break only one 'for', that is go back
to 5th line in the example code (directory C has one empty file):

> for line in f:

^^^

> line = line.rstrip()
if "PRIMARY" not in line:
j += 1
if j == 20:
break
else:
for line in f:

^^^
You're iterating through the same value in inner and outer loop.
Don't do that. It's hard to predict the behavior of such a code.

Regarding break statement, it breaks only the inner loop
and returns to the outer loop/block.

It would be great if you could reduce your code to a short piece
that illustrates your problem and that we could all run.

I ended up using another method as someone suggested to me. I am still
not sure why the previous version got stuck on empty files, while this
one doesn't:

receptors = ['A' 'B']
for x in receptors:
# open out_file for appending for each 'x' in receptors, close at
same level
out_file =
open('c:/Linux/Dock_method_validation/%s/validation/pockets.out' %(x),'a')
for i in range(10):
for r in (7, 9, 11, 13, 15, 17):
f =
open('c:/Linux/Dock_method_validation/%s/validation/ligand_ran_line_%s_%sA_secondary_scored.mol2'
%(x,i,r), 'r')
# assume 'PRIMARY' should be found first
# set flag for string 'PRIMARY'
primary = False
# iterate on file object, empty files will be skipped
for line in f:
if 'PRIMARY' in line:
primary = True
out_file.write(line.strip())
# copy scores
elif 'TRIPOS' not in line and primary:
out_file.write(line.strip())
out_file.write(' ')
elif 'TRIPOS' in line and primary:
break
print
out_file.write('\n')
f.close()
out_file.close()

[Scott David Daniels]

Ben Keshet wrote:
....

I ended up using another method as someone suggested to me. I am still
not sure why the previous version got stuck on empty files, while this
one doesn't:

receptors = ['A' 'B']

*** Alarm bells *** Do you mean ['AB'], or do you mean ['A', 'B']?

...(more code one way) ...

Don't be afraid of defining functions, you are nested too deeply to
easily understand, and hence likely to make mistakes. For similar
reasons, I don't like names like x and i unless there are no better
names. Also, since you don't seem to "really" need to write, I used
print. The comments would be better if I knew the field a bit (or
your code had had better names).
Try something like (obviously I couldn't test it, so untested code):

OUTPUT = 'c:/Linux/Dock_method_validation/%s/validation/pockets.out'
INPUT = ('c:/Linux/Dock_method_validation/%s/validation/'
'ligand_ran_line_%s_%sA_secondary_scored.mol2')

def extract_dist(dest, receptor, line, ligand):
'''Get distances after "PRIMARY" from the appropriate file
'''
source = open(INPUT % (receptor, line, ligand), 'r')
gen = iter(source) # get a name for walking through the file.
try:
# Find the start
for j, text in enumerate(gen):
if 'PRIMARY' in text:
print >>dest, text.strip(),
break
if j == 19: # Stop looking after 20 lines.
return # nothing here, go on to the next one
# copy scores up to TRIPOS
for text in gen:
if 'TRIPOS' in text:
break
print >>dest, text.strip(),
print
print >>dest
finally:
source.close()

for receptor in 'A', 'B':
# open out_file for appending per receptor, close at same level
out_file = open(OUTPUT % receptor, 'a')
for line in range(10):
for ligand in (7, 9, 11, 13, 15, 17):
extract_dist(out_file, receptor, line, ligand)
out_file.close()
--Scott David Daniels
Sc***********@Acm.Org