[Tutor] Text Processing Query

[Bod Soutar]

On 14 March 2013 10:56, Spyros Charonis <s.charonis at gmail.com> 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
>
>
> 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
>
>
>

This is how I would do it.

with open(filename) as file:
    scanfile = file.readlines()
    wanted = "CHAIN:"
    unwanted = [" A", " B"]
    for line in scanfile:
        for item in unwanted:
            if item not in line and wanted in line:
                print line

HTH,
Bodsda