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#!/bin/bash -ve
if [ ! -e genome.fasta ]; then
gunzip -c genome.fasta.gz > genome.fasta
fi
if [ ! -e pasa_assemblies.fasta ]; then
gunzip -c pasa_assemblies.fasta.gz > pasa_assemblies.fasta
fi
if [ ! -e pasa_assemblies.gff3 ]; then
gunzip -c pasa_assemblies.gff3.gz > pasa_assemblies.gff3
fi
if [ ! -e pasa_assemblies_described.txt ]; then
gunzip -c pasa_assemblies_described.txt.gz > pasa_assemblies_described.txt
fi
# get the gene-to-transcript relationships
cut -f2,3 pasa_assemblies_described.txt > pasa.gene_trans_map.txt
../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -O pasa.transdecoder_workdir
../../TransDecoder.Predict -t pasa_assemblies.fasta $ARGS -O pasa.transdecoder_workdir
../../util/cdna_alignment_orf_to_genome_orf.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.gff3 pasa_assemblies.gff3 pasa_assemblies.fasta > pasa_assemblies.fasta.transdecoder.genome.gff3
../../util/fasta_prot_checker.pl pasa.transdecoder_workdir/pasa_assemblies.fasta.transdecoder.pep
echo "Done. See pasa_assemblies.fasta.transdecoder.\*"
exit 0
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