ciona savi source edited

ciona savignyi added

MIM now needs three files the genemap file to get the list of valis gene numbers, the morbidmap fiel to get a list of valid morbid map number and omim.txt to get the descriptions etc for both

get_all_Genes causing $load_transcripts flag to be misinterpreted as
the dbtype

added cleanup_tmpfiles(), create_tmpdir() can set directory, only create files that don't exist already

Changed to use gene tree homologies, and to only use homologies of type "ortholog_one2one" and "apparent_ortholog_one2one". Should avoid many-many etc.

Also set status of the gene's transcripts.