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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