file2line

#!/bin/bash
#PBS -l nodes=1:ppn=4

#### usage ####
usage() {
	echo Program: "file2line (fetch line from file matching input value in defined column)"
	echo Author: BRIC, University of Copenhagen, Denmark
	echo Version: 1.0
	echo Contact: pundhir@binf.ku.dk
	echo "Usage: file2line -i <file> -j <string> [OPTIONS]"
	echo "Options:"
	echo " -i <file>   [input tab delimited file (can be stdin)]"
    echo " -j          [string to match]"
    echo "[OPTIONS]"
    echo " -c          [column in which string to be match (default: anywhere)]"
    echo " -h          [help]"
    echo "[NOTE]"
    echo " Solves following problem: grep -w 1 <file> returns both 1 as well as 10, 11 etc"
	echo
	exit 0
}

#### parse options ####
while getopts i:j:c:h ARG; do
    case "$ARG" in
    i) INFILE=$OPTARG;;
    j) PATTERN=$OPTARG;;
    c) COLUMN=$OPTARG;;
    h) HELP=1;;
    esac
done

## usage, if necessary file and directories are given/exist
if [ -z "$INFILE" -o -z "$PATTERN" -o "$HELP" ]; then
	usage
fi

if [ ! -z "$COLUMN" ]; then
    if [ "$INFILE" == "stdin" ]; then
        while read LINE; do
            echo ${LINE}
        done
    else
        zless $INFILE 
    fi | perl -ane 'if($_!~/^#/) { if($F['$((COLUMN-1))']=~/^'$PATTERN'$/) { print $_; } }'
else 
    if [ "$INFILE" == "stdin" ]; then
        while read LINE; do
            echo ${LINE}
        done
    else
        zless $INFILE 
    fi | perl -ane 'if($_!~/^#/) { if($_=~/\s+'$PATTERN'\s+/) { print $_; } }'
fi