arrangePPOutput: This function arrange the phyloprofile output of the...
In giangnguyen0709/fCAT: fCAT

This function arrange the phyloprofile output of the interested genome into the corresponding folder in the output folder

arrangePPOutput(
  ppOutputList,
  refSpecList,
  output,
  coreSet,
  genomeName,
  scoreMode,
  extend
)

`ppOutputList`	a list contains the phylogenetic profile of the interested genome in data.frame, the fasta file of the genome in vector, 2 file domains of the genome in data.frame (two file domains can be NULL) #' @param refSpecList 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.
`output`	The directory which contains the output directory
`coreSet`	The name of the interested core set. The core directory can contains more than one core set and the user must specify the interested core set. The core set will be stored in the folder core_orthologs in subfolder, specify them by the name of the subfolder
`genomeName`	the name of the interested genome
`scoreMode`	the mode determines the method to scoring the founded ortholog and how to classify them. Choices: 1, 2, 3, "busco"
`extend`	The output of the function is a phylogenetic profile of the interested genome. It contains 4 files, .phyloprofile, .extended.fa, _reverse.domains and _forward.domains. If extend = TRUE, the files will be appended into the old files in the folder output of the core directory or in the inputed folder by the user with the argument ppDir. If there is no old files in the folder, the output files of the function will be writen in the new files.