console controller load folder now looks only for path + genome.fasta / genome.gff; does not automatically print stats on load
console now handles telling you that the genome is loaded.
no more writing trinotate, since we're no longer reading it
we now write 'genome.fasta', 'genome.tbl', etc. since we now look for those filenames...
added sequence.cds_to_gff
added gene.contains_mrna()
more tests for gene.contains_mrna
added gene.cds_to_gff
more tests for gene.cds_to_gff
added mrna.cds_to_gff
removed strand argument from genepart, cds, exon to_gff methods
added 'seq_id' to arguments for gene.cds_to_gff, added seq_id and source to its call to mrna.cds_to_gff, what a mess
seq now passes its header to gene.cds_to_gff
mrna now passes necessary arguments to cds.to_gff
mrna.to_gff no longer takes strand since it knows its strand now. it also no longer passes strand to cds, exon or other_feature
gene no longer passes its strand down for to_gff calls
gene_part no longer takes strand in to_tbl
exon no longer takes strand in to_tbl
mrna no longer passes strand down to cds, exon in to_tbl call
mrna no longer takes strand as an argument in to_tbl