#!/usr/bin/env -S awk -f
# Filter out 'supercontigs' records
# from an Ensembl proteome fasta file
# Usage:
# awk -f remove_supercontigs.awk \
# "proteome.fasta" \
# > "proteome_nosupercontigs.fasta"

BEGIN {
    on_good_sequence = 0
}

/^>/ {
    on_good_sequence = 0
    locus = $3
    split(locus, locus_array, ":")
    if (locus_array[1] != "supercontig") {
        on_good_sequence = 1
        print $0
    }
}

/^[^>]/ && on_good_sequence {
    print $0
}