getSpec: The function read the fasta file in each core gene and...
In giangnguyen0709/fCAT: fCAT

Description Usage Arguments Value Examples

The function read the fasta file in each core gene and extract the references species based on the priority order in the priority list. The function search in the fasta file to find the refererences species in priority order of the list. If no references taxon is determined, the function returns NULL

1	getSpec(fasta, priorityList)

`fasta`	the path to the fasta file in the core gene
`priorityList`	A list contains one or many genome ID of the genomes, which were used to build the core set. The genome ID of this list will be stored with an priority order, the tool look at into the fasta file of each core group and determine with the priority order to determine the references species for each core group.

The function will return the references species. If the function did not find any references species, it will return the value NULL

coreFolder <- system.file("extdata", "sample", package = "fCAT")
fasta <- paste(coreFolder, "/core_orthologs/test/530670/530670.fa", sep = "")
refSpec <- getSpec(fasta, c("HUMAN@9606@1"))
print(refSpec)