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# Katharina J. Hoff
# April 5th 2018
# Example data set for demonstration of AUGUSTUS UTR training
# Downloaded NCBI genes from UCSC genome browser for dm6 via table browser -> genes_with_utrs.gtf
ucsc_gtf2gff3.pl --in=genes_with_utrs.gtf --out=genes_with_utrs.gff3
cat genes_with_utrs.gff3 | perl -pe "s/five_prime_utr/5'-UTR/; s/three_prime_utr/3'-UTR/;" > genes_with_utrs.f.gff3
cat genes_with_utrs.f.gff3 | perl -ne 'if(not($_=~m/\tgene\t/) and not($_=~m/\tmRNA\t/)){
@t = split(/\t/); print "$t[0]\t$t[1]\t$t[2]\t$t[3]\t";
print "$t[4]\t$t[5]\t$t[6]\t$t[7]\t"; $_=~m/Parent=(\S+)/; print "gene_id \"$1\"; transcript_id \"$1\";\n";
}' > genes_with_utrs.gtf
# Downloaded genome from UCSC dm6
gunzip dm6.fa.gz
cdbfasta dm6.fa -o dm6.fa.idx
cdbyank dm6.fa.idx -d dm6.fa -a chr2R > genome.fa
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