12-01-2009
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
[options] file1 file2
DESCRIPTION
forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 or file2 is the standard
input is used.
file1 and file2 must be sorted in increasing collating sequence (see Environment Variables below) on the fields on which they are to be
joined; normally the first in each line.
The output contains one line for each pair of lines in file1 and file2 that have identical join fields. The output line normally consists
of the common field followed by the rest of the line from file1, then the rest of the line from file2.
The default input field separators are space, tab, or new-line. In this case, multiple separators count as one field separator, and lead-
ing separators are ignored. The default output field separator is a space.
Some of the below options use the argument n. This argument should be a or a referring to either file1 or file2, respectively.
Options
In addition to the normal output,
produce a line for each unpairable line in file n, where n is or
Replace empty output fields by string
s.
Join on field
m of both files. The argument m must be delimited by space characters. This option and the following two are provided for
backward compatibility. Use of the and options ( see below ) is recommended for portability.
Join on field
m of file1.
Join on field
m of file2.
Each output line comprises the fields specified in
list, each element of which has the form where n is a file number and m is a field number. The common field is not printed
unless specifically requested.
Use character
c as a separator (tab character). Every appearance of c in a line is significant. The character c is used as the field sepa-
rator for both input and output.
Instead of the default output,
produce a line only for each unpairable line in file_number, where file_number is or
Join on field
f of file 1. Fields are numbered starting with 1.
Join on field
f of file 2. Fields are numbered starting with 1.
EXTERNAL INFLUENCES
Environment Variables
determines the collating sequence expects from input files.
determines the alternative blank character as an input field separator, and the interpretation of data within files as single and/or multi-
byte characters. also determines whether the separator defined through the option is a single- or multi-byte character.
If or is not specified in the environment or is set to the empty string, the value of is used as a default for each unspecified or empty
variable. If is not specified or is set to the empty string, a default of ``C'' (see lang(5)) is used instead of If any internationaliza-
tion variable contains an invalid setting, behaves as if all internationalization variables are set to ``C'' (see environ(5)).
International Code Set Support
Single- and multi-byte character code sets are supported with the exception that multi-byte-character file names are not supported.
EXAMPLES
The following command line joins the password file and the group file, matching on the numeric group ID, and outputting the login name, the
group name, and the login directory. It is assumed that the files have been sorted in the collating sequence defined by the or environment
variable on the group ID fields.
The following command produces an output consisting all possible combinations of lines that have identical first fields in the two sorted
files sf1 and sf2, with each line consisting of the first and third fields from and the second and fourth fields from
WARNINGS
With default field separation, the collating sequence is that of with the sequence is that of a plain sort.
The conventions of and are incongruous.
Numeric filenames may cause conflict when the option is used immediately before listing filenames.
AUTHOR
was developed by OSF and HP.
SEE ALSO
awk(1), comm(1), sort(1), uniq(1).
STANDARDS CONFORMANCE
join(1)