USAGE

Required:

 -t <string>                            transcripts.fasta

Optional:

 --gene_trans_map <string>              gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> ) 
 -m <int>                               minimum protein length (default: 100)
 
 -G <string>                            genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia)
 -S                                     strand-specific (only analyzes top strand)
 -p <int>                               shorten potential 5' partials if they are this percentage of the original protein or longer.

Genetic Codes

See <http://golgi.harvard.edu/biolinks/gencode.html>. These are currently supported:

 universal (default)
 Euplotes
 Tetrahymena
 Candida
 Acetabularia
 Mitochondrial-Canonical
 Mitochondrial-Vertebrates
 Mitochondrial-Arthropods
 Mitochondrial-Echinoderms
 Mitochondrial-Molluscs
 Mitochondrial-Ascidians
 Mitochondrial-Nematodes
 Mitochondrial-Platyhelminths
 Mitochondrial-Yeasts
 Mitochondrial-Euascomycetes
 Mitochondrial-Protozoans