Just search for species instead of species+genes

[boopsboops]

Perhaps faster if only search for species names instead of adding the gene names to the exhaustive search? Potentially fewer queries, but a bigger fasta download that includes all non-mtDNA. Could be simpler?

See code here:

# choose exhaustive or simple search for number of strings to search
if(opt$exhaustive == "true") {
    query <- paste0("(",spp.list,"[ORGN] AND ",range,"[SLEN])")
} else if (opt$exhaustive == "false") {
    gene.syns <- "(mitochondrial[ALL] OR mitochondrion[ALL])"
    query <- unlist(mapply(function(x) paste0("(",spp.list,"[ORGN] AND ",x," AND ",range,"[SLEN])"), gene.syns, SIMPLIFY=FALSE, USE.NAMES=FALSE))
} else stop(writeLines("'-e' value must be 'true' or 'false'."))

[boopsboops]

Seems that this consistently maxes out the limit of records, even with a low -q value of 500.

Need to rethink.