Shell Programming and Scripting

sample1 A
sample2 B
sample3 B
sample4 C
sample5 A
sample6 D
sample7 D

sample1 sample2 sample3 sample4 sample5 sample6 sample7
chr start end a1 b1 c1 a2 b2 c2 a3 b3 c3 a4 b4 c4 a5 b5 c5 a6 b6 c6 a7 b7 c7
chr start end d1 e1 f1 d2 e2 f2 d3 e3 f3 d4 e4 f4 d5 e5 f5 d6 e6 f6 d7 e7 f7

sample2 sample3 sample6 sample7
chr start end a2 b2 c2 a3 b3 c3 a6 b6 c6 a7 b7 c7 
chr start end d2 e2 f2 d3 e3 f3 d6 e6 f6 d7 e7 f7

(with header, multiple rows and cols, each sample has 3 values a,b,c)

(no header first 3 cols)

sample2 B
sample3 B
sample6 D
sample7 D

sample2 sample3 sample6 sample7
chr start end a2 b2 c2 a3 b3 c3 a6 b6 c6 a7 b7 c7 
chr start end ....

(no header first 3 cols)

#!/bin/ksh
# Usage: tester key...
# This script will look for any "key" given on the command line as a value in
# field 2 of File1 and then extract data from File2 based on the headings
# specified by field 1 of File1.
if [ $# -lt 1 ]
then    echo "Usage; ${0##*/} key..." >&2
        exit 1
fi
errf=stderr.$$
if ! printf "%s\n" "$@" | awk -v errf="$errf" '
FNR == 1 {
        # Increment input file count.
        # f == 1 => List of keys.
        # f == 2 => File1
        # f == 3 => File2
        f++
}
f == 1 {keys[$0]        # Save the keys
        next
}
f == 2 && $2 in keys {  # Save headers to be extracted from File2.
        headers[$1]
        next
}
f == 3 && FNR == 1 {    # 1st line of File2; create list of sets of fields to
                        # extract from remaining lines
        fields[1]       # Always keep 1st three fields
        fields[2]
        fields[3]
        for(i = 1; i<= NF; i++) {
                if($i in headers) {
                        # We have a matching header, add corresonding fields to
                        # the extraction list.
                        fields[3 * i + 1]
                        fields[3 * i + 2]
                        fields[lf = 3 * i + 3]  # Save last field #.
                        printf("%s%s", nh++ ? " " : "", $i)
                }
        }
        if(nh == 0) {   # No headers found.  Print diagnostic message.  It is
                        # being saved in a file since there is no portable way
                        # to direct output from awk to stderr.  The calling
                        # shell script will copy the message to stderr and add
                        # the script name to the start of the diagnostic.
                print ": Headings identified by keys not found in File2." > errf
                exit 1
        }
        print ""        # Add a trailing newline to the output file headings.
        next
}
{       for(i = 1; i <= NF; i++)        # Print selected fields from remaining
                if(i in fields) # lines in File2.
                        printf("%s%s", $i, i == lf ? "\n" : " ")
}' - File1 File2 > File3
then    # awk failed, print diagnostic message.
        printf "%s" ${0##*/} >&2
        cat $errf >&2
        rm $errf
        exit 1
fi

chmod +x tester

./tester B D

./tester D B

sample2 sample3 sample6 sample7
chr start end a2 b2 c2 a3 b3 c3 a6 b6 c6 a7 b7 c7
chr start end d2 e2 f2 d3 e3 f3 d6 e6 f6 d7 e7 f7