awk_for_kate

# Create a file with the awk code
echo '
$6 == "protein_coding" {
    gene_counter[$10] += 1
}

END {
    for (gene_name in gene_counter){
        print gene_name, gene_counter[gene_name]
    }
}' > gene_counter.awk

# run the code again
awk -F "\t" '$3 == "exon" { print $9 }' transcriptome.gtf | \
tr -d ";\"" | \
awk -F " " -f gene_counter.awk > number_of_exons_by_gene.txt

# see if it works now
head number_of_exons_by_gene.txt