Question: setting database.path for extracting PSSM Feature in BioSeqClass
gravatar for greensandag
3.8 years ago by
greensandag0 wrote:

How can i use Feature PSSM in BioSeqClass packages?. i tried run this program:


  file = file.path(path.package("BioSeqClass"), "example", "acetylation_K.fasta")
  tmp = readAAStringSet(file)
  proteinSeq = as.character(tmp)
  ## Need "blastpgp" program and a formated database. Database can be formated by "formatdb" program.
  PSSM1 = featurePSSM(proteinSeq[1:2], start.pos=rep(1,2), stop.pos=rep(10,2), psiblast.path="blastpgp", database.path="./result1.fasta")


but, i got  error messages:

Error in featurePSSM(proteinSeq[1:2], start.pos = rep(1, 2), stop.pos = rep(10,  : 
  Do not have formated database file: ./


How can i setting database.path? if my directory for database : C:\BLAST\db

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