[Tutor] Text Processing Query

[Prasad, Ramit]

Spyros Charonis wrote:
> Hello Pythoners,
> 
> I am trying to extract certain fields from a file that whose text looks like this:
> 
> COMPND   2 MOLECULE: POTASSIUM CHANNEL SUBFAMILY K MEMBER 4;
> COMPND   3 CHAIN: A, B;
> 
> COMPND  10 MOL_ID: 2;
> COMPND  11 MOLECULE: ANTIBODY FAB FRAGMENT LIGHT CHAIN;
> COMPND  12 CHAIN: D, F;
> COMPND  13 ENGINEERED: YES;
> COMPND  14 MOL_ID: 3;
> COMPND  15 MOLECULE: ANTIBODY FAB FRAGMENT HEAVY CHAIN;
> COMPND  16 CHAIN: E, G;
> 
> I would like the chain IDs, but only those following the text heading "ANTIBODY FAB FRAGMENT", i.e. I
> need to create a list with D,F,E,G  which excludes A,B which have a non-antibody text heading. I am
> using the following syntax:
> 
> with open(filename) as file:
>     scanfile=file.readlines()
>     for line in scanfile:
>         if line[0:6]=='COMPND' and 'FAB FRAGMENT' in line: continue
>         elif line[0:6]=='COMPND' and 'CHAIN' in line:
>             print line

There is no reason to use readlines in this example, just
iterate over the file object directly. 

 with open(filename) as file:
     for line in file:
         if line[0:6]=='COMPND' and 'FAB FRAGMENT' in line: continue
         elif line[0:6]=='COMPND' and 'CHAIN' in line:
             print line


> 
> But this yields:
> 
> COMPND   3 CHAIN: A, B;
> COMPND  12 CHAIN: D, F;
> COMPND  16 CHAIN: E, G;
> 
> I would like to ignore the first line since A,B correspond to non-antibody text headings, and instead
> want to extract only D,F & E,G whose text headings are specified as antibody fragments.
> 
> Many thanks,
> Spyros
> 

Will 'FAB FRAGMENT' always be the line before 'CHAIN'? 
If so, then just keep track of the previous line. 

>>> raw
'COMPND   2 MOLECULE: POTASSIUM CHANNEL SUBFAMILY K MEMBER 4;\nCOMPND   3 CHAIN: A, B;\nCOMPND  10 MOL_ID: 2;\nCOMPND  11 MOLECULE: \
ANTIBODY FAB FRAGMENT LIGHT CHAIN;\nCOMPND  12 CHAIN: D, F;\nCOMPND  13 ENGINEERED: YES;\nCOMPND  14 MOL_ID: 3;\nCOMPND  15 MOLECULE\
: ANTIBODY FAB FRAGMENT HEAVY CHAIN;\nCOMPND  16 CHAIN: E, G;'

>>> prev = ''
>>> chains = []
>>> for line in raw.split('\n'):
...     if 'COMPND' in prev and 'FAB FRAGMENT' in prev and 'CHAIN' in line:
...         chains.extend( line.split(':')[1].replace(',','').replace(';','').split())
...     prev = line
...     
>>> chains
['D', 'F', 'E', 'G']


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