[Tutor] how to read two files and substitute

[lina]

$ python atomToResidues.py
Traceback (most recent call last):
  File "atomToResidues.py", line 6, in <module>
    mapping[parts[1]]=parts[4]
IndexError: list index out of range

Following Michiel's code (a little adjustment was done):

#!/bin/python

mapping={}
for line in open("confout.pdb").readlines():
   parts=line.strip().split()
   mapping[parts[1]]=parts[4]
origs=open("dummy.atomID").read().split()
print " ".join([mapping[orig] for orig in origs])



On Tue, May 17, 2011 at 11:12 PM, lina <lina.lastname at gmail.com> wrote:
> Thanks all first,
>
> I wrote a .bash, but not work.
>
> for python one, I am not confident in writing one. I will try Michiel one now.
>
>
>
> On Tue, May 17, 2011 at 10:19 PM, Emile van Sebille <emile at fenx.com> wrote:
>> On 5/17/2011 6:42 AM lina said...
>>>
>>> Hi,
>>>
>>> For file1:
>>>
>>>   5007  O28 CHO   173      35.300  99.430  65.810  1.00  0.0
>>>   5008  H29 CHO   173      35.680 100.290  66.150  1.00  0.00
>>>   5009  C1  CHO   174      59.060  12.440  58.680  1.00  0.00
>>>   5010  C2  CHO   174      59.460  12.480  60.160  1.00  0.00
>>>   5011  C3  CHO   174      59.590  11.120  60.830  1.00  0.00
>>>   5012  C4  CHO   174      60.780  10.430  60.160  1.00  0.00
>>>
>>> For file2:
>>>
>>> 5008 5010 5011
>>>
>>> I want to get the $4(column 4) value which has  the $1 value. for
>>> values in file2
>>>
>>> such as the results is 173 174 174
>>>
>>> Thanks for any suggestions,
>>>
>>
>>
>> It'll help us help you if you show how far along you've come. Otherwise,
>> most of us will presume this is a homework assignment, and we'd rather help
>> you learn python than do your homework for you.
>>
>> In short, you'll read the lines from the file, test each line to see if it
>> starts with one of the targets, then spilt the fields from the line and
>> select the fourth field.  Accumulate those and return the result.
>>
>> Post your code when you follow up please.
>>
>> Emile
>>
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>
>
>
> --
> Best Regards,
>
> lina
>



-- 
Best Regards,

lina