fill_blast_result: Complement BLAST result

fill_blast_resultR Documentation

Complement BLAST result


Provides subjects' GenInfo Identifiers if BLAST alignment result does not contain one.


  blast.result, = "Racc", = "Rgi",
  delete.version = FALSE,
  version.sep = ".", = "DB",,
  temp.db = NULL,
  delete.temp = FALSE, = NULL, = NULL, = "AC", = "GI",
  mc.cores = 1,
  verbose = TRUE

delete_AcNum_version(ac.num.var, version.sep = ".", mc.cores = 1)



data frame; BLAST alignment result,

character; name of column with subject accession numbers and GenInfo Identifier numbers from BLAST result data frame


logical; remove version suffix from subject accession number


character; accession number and version suffix separator (a dot for NCBI accession numbers)

character; table with linked accession and GI numbers is taken from SQLite database ("DB") or data frame ("DF")

data frame with table (used if = "DF")


character; temporal SQLite database name and path


logical; delete created temporal SQLite database,,,

SQLite database name and path, table name and name of columns with accession and GI numbers (used if = "DB")


integer; number of processors for parallel computation (not supported on Windows)


logical; show messages


vector of accession numbers


BLAST alignment, performed with local database, may not contain subject GI information. Also subject accession may contain version suffix. This can make it difficult to analyze the results further. This function adds subject GI and removes subject accession version suffix.

To add GI GenInfo Identifiers table with them linked to accession numbers must be provided as data frame or SQLite database table. must be a data frame with column one - accession numbers, column two - GenInfo Identifier numbers. If = "DF" temporal SQLite database is created.

SQLite database table with accession and GI numbers should not contain duplicated rows. It is also highly recommended to index accession numbers' variable in database.

delete.version executes in the first step, so if you use this option accession numbers in table must not contain version suffix.,, and must be column names exactly as in data frame.


blast.result data frame with added GI and deleted accession version suffix.


  • fill_blast_results: Provides subjects' Genbank Identifiers if BALST alignment result does not contain one

  • delete_AcNum_version: Remove accession version suffix


Elena N. Filatova


path <- tempdir()
dir.create (path)
# load raw blast results
data (blast.raw)
#load with result (targets' sequences) GI and Acc.nums
data (
blast.fill <- fill_blast_results(blast.result = blast.raw, delete.version = TRUE,
                        = "DF", =[, c("GB_AcNum", "gi")],
                                 temp.db = paste0 (path, "/temp.db"), delete.temp = TRUE)

disprose documentation built on March 19, 2022, 2:15 a.m.