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Top Forums UNIX for Dummies Questions & Answers Merging two files based on two columns to make a third file Post 302517396 by 2pugs on Tuesday 26th of April 2011 04:50:08 PM
Old 04-26-2011
This may not be the most efficient way if you're files are really large but it works. Let me know if any of it is unclear.

Code:
Code:
#!/bin/bash
while read line
do
    col1=$(echo $line | awk '{print $1}')
    col2=$(echo $line | awk '{print $2}')
    row_from_file2=$(grep " $col1 " file2 | grep " $col2 ")
    file2_col2=$(echo $row_from_file2 | awk '{print $2}')
    file2_col4=$(echo $row_from_file2 | awk '{print $4}')
    if [[ "$col1" = "$file2_col2" && "$col2" = "$file2_col4" ]]
    then
        echo "Found a match"
        echo "$line $row_from_file2" >> file3
    fi
done < file1

Output:
Code:
# cat file1
chr1 10001980 T A
# cat file2
1 chr1 41980 41981 snp A G dbsnp.86:rs806721
1 chr1 41980 10001980 snp A G dbsnp.86:rs806721
# ./match_file1_file2.bash
Found a match
# cat file3
chr1 10001980 T A 1 chr1 41980 10001980 snp A G dbsnp.86:rs806721

 

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CAT(1)							    BSD General Commands Manual 						    CAT(1)

NAME
cat -- concatenate and print files SYNOPSIS
cat [-belnstuv] [file ...] DESCRIPTION
The cat utility reads files sequentially, writing them to the standard output. The file operands are processed in command-line order. If file is a single dash ('-') or absent, cat reads from the standard input. If file is a UNIX domain socket, cat connects to it and then reads it until EOF. This complements the UNIX domain binding capability available in inetd(8). The options are as follows: -b Number the non-blank output lines, starting at 1. -e Display non-printing characters (see the -v option), and display a dollar sign ('$') at the end of each line. -l Set an exclusive advisory lock on the standard output file descriptor. This lock is set using fcntl(2) with the F_SETLKW command. If the output file is already locked, cat will block until the lock is acquired. -n Number the output lines, starting at 1. -s Squeeze multiple adjacent empty lines, causing the output to be single spaced. -t Display non-printing characters (see the -v option), and display tab characters as '^I'. -u Disable output buffering. -v Display non-printing characters so they are visible. Control characters print as '^X' for control-X; the delete character (octal 0177) prints as '^?'. Non-ASCII characters (with the high bit set) are printed as 'M-' (for meta) followed by the character for the low 7 bits. EXIT STATUS
The cat utility exits 0 on success, and >0 if an error occurs. EXAMPLES
The command: cat file1 will print the contents of file1 to the standard output. The command: cat file1 file2 > file3 will sequentially print the contents of file1 and file2 to the file file3, truncating file3 if it already exists. See the manual page for your shell (e.g., sh(1)) for more information on redirection. The command: cat file1 - file2 - file3 will print the contents of file1, print data it receives from the standard input until it receives an EOF ('^D') character, print the con- tents of file2, read and output contents of the standard input again, then finally output the contents of file3. Note that if the standard input referred to a file, the second dash on the command-line would have no effect, since the entire contents of the file would have already been read and printed by cat when it encountered the first '-' operand. SEE ALSO
head(1), more(1), pr(1), sh(1), tail(1), vis(1), zcat(1), fcntl(2), setbuf(3) Rob Pike, "UNIX Style, or cat -v Considered Harmful", USENIX Summer Conference Proceedings, 1983. STANDARDS
The cat utility is compliant with the IEEE Std 1003.2-1992 (``POSIX.2'') specification. The flags [-belnstv] are extensions to the specification. HISTORY
A cat utility appeared in Version 1 AT&T UNIX. Dennis Ritchie designed and wrote the first man page. It appears to have been cat(1). BUGS
Because of the shell language mechanism used to perform output redirection, the command ``cat file1 file2 > file1'' will cause the original data in file1 to be destroyed! The cat utility does not recognize multibyte characters when the -t or -v option is in effect. BSD
January 29, 2013 BSD
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