bed2saf

#!/bin/bash

# Function to display usage message
usage() {
  echo "Usage: $0 <input.bed>"
  echo "Converts a BED file (given as input) to SAF format and prints to standard output."
  echo "Input BED format: chr, start(0), end(1), name, score, strand"
  echo "Output SAF format: GeneID, Chr, Start(1), End(1), Strand"
  exit 1
}

# Check for no arguments or help flags
if [ "$#" -ne 1 ] || [ "$1" == "-h" ] || [ "$1" == "--help" ]; then
  usage
fi

BED_FILE="$1"

# Check if input file exists and is readable
if [ ! -f "$BED_FILE" ] || [ ! -r "$BED_FILE" ]; then
    echo "Error: Input file '$BED_FILE' not found or not readable." >&2
    exit 1
fi

# Convert BED to SAF and print to stdout
# BED: $1=chr, $2=start(0), $3=end(1), $4=name, $5=score, $6=strand
# SAF: $1=GeneID, $2=Chr, $3=Start(1), $4=End(1), $5=Strand
awk 'BEGIN{FS="\t"; OFS="\t"} {print $4, $1, $2+1, $3, $6}' "$BED_FILE"