how two join and arrange two files together

Jyoti Sharma jyoti.mickey at gmail.com
Thu Jul 23 14:30:34 CEST 2009


On Thu, 23 Jul 2009 12:52:15 +0530, <amrita at iisermohali.ac.in> wrote:

>
> Hi,
>
> I have two large files:
>
> FileA
> 15 ALA H = 8.05	N = 119.31 CA = 52.18 HA = 4.52	C =
> 21 ALA H = 7.66	N = 123.58 CA = 54.33 HA = C = 179.35
> 23 ALA H = 8.78	N =  CA =  HA = C = 179.93.................
>
> and
>
> FileB
> 21 ALA  helix (helix_alpha, helix2)
> 23 ALA  helix (helix_alpha, helix3)
> 38 ALA  helix (helix_alpha, helix3)...........
>
> now what i want that i will make another file in which i will join the  
> two
> file in such a way that only matching entries will come like here 21 and
> 23 ALA is in both files, so the output will be something like:-
>
> 21 ALA H = 7.66	N = 123.58 CA = 54.33 HA = C = 179.35| 21 ALA  helix
> (helix_alpha, helix2)
> 23 ALA H = 8.78	N =  CA =  HA = C = 179.93|23 ALA  helix (helix_alpha,
> helix3)
>
> and further i will make another file in which i will be able to put those
> lines form this file based on the missing atom value, like for 21 ALA HA
> is not defined so i will put it another file based on its HA missing  
> value
> similarly i will put 23 ALA on another file based on its missing N,CA and
> HA value.
>
> I tried to join the two file based on their matching entries by:---

(snip)

I believe there are packages available for doing such things mostly  
written in perl. But if the aim is not to develop suitable applications  
but only to obtain the desired formatted file then doing this with the  
help of something like Excel would be easiest. This is my opinion from the  
experience I have from my bioinfo programming.

Regards,
Jyoti



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