#Generate Trinotate Report Script
#Requires blastx, blastp, hmmscan, signalp and tmhmm results

#Commands that have been run
#./TransDecoder.LongOrfs -t ~/sample.fasta
#./TransDecoder.Predict -t ~/sample.fasta
#gunzip Pfam-A.hmm.gz 
#hmmpress Pfam-A.hmm 
#hmmscan --domtblout TrinotatePFAM.out ./Trinotate/admin/Pfam-A.hmm sample.fasta.transdecoder.pep
#blastx -db mini_swissprot -query sample.fasta -outfmt 6 -evalue 1e-5 -max_target_seqs 1 > swissprot.blastx.out
#blastp -db mini_swissprot -query sample.fasta.transdecoder.pep -outfmt 6 -evalue 1e-5 -max_target_seqs 1 > swissprot.blastp.out
#signalp -f short -n signalp.out sample.fasta.transdecoder.pep
#tmhmm --short < sample.fasta.transdecoder.pep > tmhmm.out
#cp ./Trinotate/admin/Trinotate.sqlite Trinotate.sqlite
chmod +w Trinotate.sqlite
./Trinotate Trinotate.sqlite init --gene_trans_map gene_trans_map --transcript_fasta sample.fasta --transdecoder_pep sample.fasta.transdecoder.pep
./Trinotate Trinotate.sqlite LOAD_swissprot_blastp swissprot.blastp.outfmt6
./Trinotate Trinotate.sqlite LOAD_swissprot_blastx swissprot.blastx.outfmt6
./Trinotate Trinotate.sqlite LOAD_pfam TrinotatePFAM.out
./Trinotate Trinotate.sqlite LOAD_tmhmm tmhmm.out
./Trinotate Trinotate.sqlite LOAD_signalp signalp.out
./Trinotate Trinotate.sqlite report > Trinotate.xls