Messy little script to run local BLAST against 16S database

16S_Local-BLAST.rmd

---
title: "16S"
author: "Chase Clark"
date: "May 15, 2018"
output: html_document
---

```{r eval=FALSE}
# download file
#download.file(url = "ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz", destfile = "16SMicrobial.tar.gz", mode = 'wb')

# extract files from zipped file
#untar("16SMicrobial.tar.gz", exdir = "data/16S/blast_16SMicrobial_db")

```

```{r eval=FALSE}
Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:/Program Files/NCBI/blast-2.7.1/bin", sep= .Platform$path.sep))
bacteria16Sdatabase <- blast(db = "data/16S/blast_16SMicrobial_db/16SMicrobial")  # create rBLAST database connection

sequences <- Biostrings::readDNAStringSet("data/16S/16S_fasta.fas", "fasta") # read in fasta

multiBLAST <- function(seqs, database = bacteria16Sdatabase, keep = 0.95){
  
  seq_pred <- NULL
    # use rBLAST and add sequence to subsequent dataframe
  for (i in seq_along(seqs)){
  predict(database, seqs[i]) %>% # run blastn
  dplyr::top_n(5) %>% 
  dplyr::mutate_at(., c('QueryID', 'SubjectID'), as.character) %>%  # change to character
  dplyr::bind_rows(seq_pred, .) ->
seq_pred      
  
  }
  
  
  # return dataframe  
  return(seq_pred)
}

blastResults <- multiBLAST(sequences) # run multiBLAST function defined above

blastResults <- as_tibble(blastResults)
saveRDS(blastResults,"data/16S/LocalBlast/blastResults.rds")
      
```