new python user needs help!

**bvdet** · Apr 11 '08, 02:37 AM

Please use code tags. The code is difficult to follow without them. You can accomplish your needs with much less code. Reading the file and splitting the data if fairly straightforward , and so is formatting the output if you use some of the tools Python has available. The following reads the data into two lists - header and acid data:
[code=Python]acids = 'ACDEFGHIKLMNPQ RSTVXYW'
num_range = [10,22]
fn = r'H:\TEMP\temsy s\amino_acids_d ata.txt'
f = open(fn)

# save the header text list using a list comprehension
headerList = [item.strip() for item in f.readline()[1:].split()]
print headerList

# save stripped lines in a list using a list comprehension
lineList = [item.strip() for item in f]
f.close()[/code]The next section formats the results for printing.[code=Python]
# iterate on list of lines without the list comprehensions
for item in lineList:
itemList = item.split()
acid = itemList[1]
z_coord = float(itemList[-1])
print 'True/False A C D E F G H I K L M N P Q R S T V X Y W'
if num_range[0]<=abs(z_coord)< =num_range[1]:
print 1,
else:
print -1,
outputList = []
for letter in acids:
if acid == letter:
outputList.appe nd('1:%d' % (acids.index(le tter)+1))
else:
outputList.appe nd('0:%d' % (acids.index(le tter)+1))
print ' '.join(outputLi st)[/code]The following does the same thing, but uses list comprehensions:[code=Python]# iterate on list of lines
for item in lineList:
itemList = item.split()
acid = itemList[1]
z_coord = float(itemList[-1])
print 'True/False A C D E F G H I K L M N P Q R S T V X Y W'
print '%d' % ([-1, 1][(num_range[0]<=abs(z_coord)< =num_range[1]) or 0]),
print ' '.join(['%d:%d' % ([0, 1][acid==letter or 0], acids.index(let ter)+1) for letter in acids])[/code]Sample output:
[code=Python]
>>> True/False A C D E F G H I K L M N P Q R S T V X Y W
-1 1:1 0:2 0:3 0:4 0:5 0:6 0:7 0:8 0:9 0:10 0:11 0:12 0:13 0:14 0:15 0:16 0:17 0:18 0:19 0:20 0:21
True/False A C D E F G H I K L M N P Q R S T V X Y W
-1 0:1 0:2 0:3 0:4 0:5 0:6 0:7 0:8 0:9 0:10 0:11 0:12 0:13 0:14 0:15 0:16 0:17 1:18 0:19 0:20 0:21
True/False A C D E F G H I K L M N P Q R S T V X Y W
1 0:1 0:2 0:3 0:4 0:5 0:6 1:7 0:8 0:9 0:10 0:11 0:12 0:13 0:14 0:15 0:16 0:17 0:18 0:19 0:20 0:21[/code]It looks like there are 21 acids.

**drjekil** · Apr 23 '08, 09:38 PM

Thanks for ur help!
sorry to answer u late.
still i have some problem...

python ffff.py
[]
True/False A C D E F G H I K L M N P Q R S T V X Y W
Traceback (most recent call last):
File "ffff.py", line 50, in <module>
if num_range[0]<=abs(zcoord)<= num_range[1]:
TypeError: bad operand type for abs(): 'list'
bash-3.1$

some times got comment like "zcoord" is not defined.If i creat a list named zcoord then got only one line output.and another thing is aminoacid position need to be printed first like 1:0,2:0,3:1,4:0 and so on.

waiting for ur help!
Thanks again!

**jlm699** · Apr 24 '08, 01:16 PM

Originally posted by drjekil

TypeError: bad operand type for abs(): 'list'

This line is telling you that the abs() command is being passed a list object instead of a single element. Right before the line insert a print command to check what you're passing to this function and try and see if you can't realize your mistake then.

new python user needs help!

new python user needs help!

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