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#!/bin/bash
if [ ! -e Trinity.fasta ]; then
gunzip -c Trinity.fasta.gz > Trinity.fasta
gunzip -c genome_alignments.gmap.gff3.gz > genome_alignments.gmap.gff3
fi
../../TransDecoder.LongOrfs -t Trinity.fasta $*
../../TransDecoder.Predict -t Trinity.fasta
# gmap was used to align the Trinity.fasta transcripts to the genome,
# using the gmap '-f 3' output formatting parameter, generating file 'genome_alignments.gmap.gff3'
../../util/cdna_alignment_orf_to_genome_orf.pl Trinity.fasta.transdecoder.gff3 genome_alignments.gmap.gff3 Trinity.fasta > Trinity.fasta.transdecoder.genome.gff3
../../util/fasta_prot_checker.pl Trinity.fasta.transdecoder.pep
exit 0
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