ppi.matchUniprot: PPI: Match Protein Sequences to UniProt
In egmg726/crisscrosslinker: An R package for protein interaction analysis

This function matches the protein sequence indeces to those in UniProt if the protein sequences used were different.

ppi.matchUniprot(
  xlink_df,
  fasta_file,
  protein_to_uniprot_id = NULL,
  fasta_directory = NULL,
  download_fasta = FALSE,
  export_matches = FALSE,
  remove_na = FALSE,
  time_out = NULL,
  canonical = FALSE
)

`xlink_df`	data.frame() as created by ppi.combineData()
`fasta_file`	FASTA file as read by seqinr::read.fasta(). Protein names must correspond to those in xlink_df.
`protein_to_uniprot_id`	Can be either path to table or data.frame. Table containing three columns: ProteinName, UniProtID, and UniProtSeq (optional). When entered, will use these IDs instead of BLAST search.
`fasta_directory`	Directory where the stored FASTA files are located. Defaults to NULL.
`download_fasta`	If TRUE, will download the found UniProt FASTA files as .fasta files to your directory. Defaults to FALSE.
`export_matches`	If TRUE, will export matches from BLAST (swissprot) search as a .csv file for later use. Defaults to FALSE.
`remove_na`	If TRUE, will remove all NAs generated by non-matches in the xlink_df output. Defaults to FALSE.
`time_out`	Integer indicating number of seconds bio3d::blast.pdb() will run before timeout. Defaults to NULL.
`canonical`	If TRUE, will ignore the isoform number (if applicable). Defaults to FALSE.