Join 2 files with multiple columns: awk/grep/join? Post: 302376539

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Top Forums UNIX for Dummies Questions & Answers Join 2 files with multiple columns: awk/grep/join? Post 302376539 by InfoSeeker on Tuesday 1st of December 2009 04:06:38 PM

12-01-2009

Registered User

Join 2 files with multiple columns: awk/grep/join?

Hello,
My apologies if this has been posted elsewhere, I have had a look at several threads but I am still confused how to use these functions. I have two files, each with 5 columns:

File A: (tab-delimited)
PDB CHAIN Start End Fragment
1avq A 171 176 awyfan
1avq A 172 177 wyfany
1c7k A 2 7 vtvtyd
1c7k A 3 8 tvtydp

File B: (tab-delimited)
PDB CHAIN Start End Fragment

1cfe A 104 109 awyfan
1cfe A 105 110 lgcgra
1dk0 A 50 55 awyfan
1d3g A 83 88 fveigs
1d3g A 84 89 vtvtyd
1dk0 A 51 56 gsqyai

I want to join the rows of two tables based on overlaps of the fifth column (column fragment). As such, the output should read:

Fragment PDB CHAIN Start End PDB CHAIN Start End
awyfan 1avq A 171 176 1cfe A 104 109
awyfan 1avq A 171 176 1dk0 A 50 55
vtvtyd 1c7k A 2 7 1d3g A 84 89

Kindly note that there can be multiple overlaps between Files A and B.

I have read of using the join function in Unix, but when I tried it I ended up with output of File A only. (I tried join -1 1 FileA FileB) based on reading a similar thread.
Alternatively, I know that I can use awk (NC=='5' I think), but I am not very familiar with the script. I know how to fgrep if the file contains a single column, but not multiple columns.
Is there a simple way to write this???

Your help will be really appreciated!
Thanks in advance!
DG

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chain

CHAIN(3)						 MBK UTILITY STRUCTURE DEFINITIONS						  CHAIN(3)

NAME

       chain - mbk lisp-like service structure

DESCRIPTION

       The chain is used for any purpose, when a list of pointer is required.  The use of this structure is strongly recommanded, when such a need
       occurs.

       The declarations needed to work on chain are available in the header file "/labo/include/mut315.h", where '315' is the actual mbk version.

       The following C structure supports the description of the chain :
	      typedef struct chain {
		 struct chain	  *NEXT;
		 void		  *DATA;
	      } chain_list;

       NEXT		   Pointer to the next chain of the list.

       DATA		   Generic pointer used to point to any kind of object. Do not forget to cast the pointer back to its previous	type  when
			   using this field.

       Remark : 	   a  specialized memory allocator has been built in order to create and free chain_lists, so absolutly avoid to create or
			   free them an other way than through the access functions.

SEE ALSO

       mbk(1), addchain(3), freechain(3), delchain(3).

BUG REPORT

       This tool is under development at the ASIM department of the LIP6 laboratory.
       We need your feedback to improve documentation and tools.

ASIM
/LIP6							  October 1, 1997							  CHAIN(3)