Intersect genes (gtf/gff) with alien_hunter output

alien_intersect.sh

#!/bin/bash

#########################################
# Anuj Sharma                           #
# [email protected]                      #
# 2022-06-24                            #
#########################################

# Reading the input parameters

OPTIND=1
OUT_FILE=""
unset -v GFF
unset -v SCO
POS="3,4,4,5"
while getopts "o:p:g:s:hv" opt; do
    case "$opt" in
        o)  OUT_FILE=$OPTARG;;
        p)  POS=$OPTARG;;
        g)  GFF=$OPTARG;;
        s)  SCO=$OPTARG;;
        h)  echo "Usage: $0  -g GFF file  -s SCO file  [-o output file] [-p column positions]" >&2 && exit 0;;
        v)  echo "$(basename $0): v0.4" >&2 && exit 0;;
        *)  echo "Extra arguments not used!" >&2
    esac
done

shift $((OPTIND-1))

# Output to STDOUT or file based on argument -o
[ ! -z $OUT_FILE ] && exec >$OUT_FILE

# Exit if necessary input are not given
[[ -z "$GFF" && -z "$SCO" ]] && echo "Input GFF and SCO files missing." >&2 && exit 1
[[ -z "$GFF" ]] && echo "Input GFF file missing." >&2 && exit 1
[[ -z "$GFF" ]] && echo "Input SCO files missing." >&2 && exit 1

# Parse SCO file into awk readable table and store as temp file
tmpfile=$(mktemp /tmp/alien_intersect.XXXXXX)
exec 3>"$tmpfile"
grep -v "score" $SCO | sed 's/\.\./\t/g' >&3

# Grab the genes within the SCO regions
#
awk -vpos=$POS '
    # Parse columns numbers for manual input
    BEGIN{split(pos,a,",")}

    # Get all start and end regions from SCO file
    NR==FNR{start[NR] = $a[1]; end[NR] = $a[2]; next;}
    
    # Loop over each region (gtf) and find genes within SCO regions
    !/^##/{for (i=1; i<=length(start); i++) {
        #check if gene falls within the region and print if it does
        if ($a[3] >= start[i] && $a[4] <= end[i]) {print $0;}
    }}

    # Break when annotation ends and sequence begins
    /^##FASTA/ {exit;}
' "$tmpfile" $GFF | uniq

# Remove temp file
rm "$tmpfile"