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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
Old 12-01-2009
Data 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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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If one of the file names is the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Input fields are normally separated spaces or tabs; output fields by space. In this case, multiple separators count as one, and leading separators are discarded. The following options are recognized, with POSIX syntax. -a n In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -v n Like -a, omitting output for paired lines. -e s Replace empty output fields by string s. -1 m -2 m Join on the mth field of file1 or file2. -jn m Archaic equivalent for -n m. -ofields Each output line comprises the designated fields. The comma-separated field designators are either 0, meaning the join field, or have the form n.m, where n is a file number and m is a field number. Archaic usage allows separate arguments for field designators. -tc Use character c as the only separator (tab character) on input and output. Every appearance of c in a line is significant. EXAMPLES
sort /adm/users | join -t: -a 1 -e "" - bdays Add birthdays to password information, leaving unknown birthdays empty. The layout of is given in users(6); bdays contains sorted lines like tr : ' ' </adm/users | sort -k 3 3 >temp join -1 3 -2 3 -o 1.1,2.1 temp temp | awk '$1 < $2' Print all pairs of users with identical userids. SOURCE
/sys/src/cmd/join.c SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b -ky,y; with -t, the sequence is that of sort -tx -ky,y. One of the files must be randomly accessible. JOIN(1)
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