makeblasttdb: Wrapper for NCBI makeblastdb

In gschofl/blastr: A wrapper for NCBI Blast

Description

Generate a BLAST database from FASTA files.

Usage

makeblasttdb(input_file, input_type = "fasta", dbtype = "nucl", ...,
  show_log = TRUE, show_cmd = FALSE)

Arguments

input_file	Input file/database name. Multiple file/database names can be provided as a character vector.
input_type	Type of data specified in input file. One of “fasta”, “blastdb”, “asn1_bin”, or “asn1_txt”.
dbtype	Molecule type of target db (“nucl” or “prot”).
...	further arguments passed to makeblastdb.
show_log	print log file.
show_cmd	print the command line instead of executing it.

See Also

Other blast functions: blastn, blastn_short, blastn_short, dc_megablast, dc_megablast, megablast, megablast; blastp, blastp_short, blastp_short; blastx; qblast; rpsblast; tblastn; tblastx

Examples

## Retrieve, for instance, the human reference genome files located at
## ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/seq/
## and generate an input file hs_ref.fa by inflating and concatenating
## the hs_ref_*.fa.gz files.
## Not run: 
makeblasttdb("hs_ref.fa", input_type = "fasta", dbtype = "nucl",
  parse_seqids = TRUE, out = "hs_ref", title = "Human reference assembly, GRCh28")

## End(Not run)

gschofl/blastr documentation built on May 17, 2019, 8:52 a.m.