blast: This function is a wrapper for the blast+ suite tools.

In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

Description

This function is a wrapper for the blast+ suite tools.

Usage

blast(blast, blast_db, input, out, e = 0.01, format = 6)

Arguments

blast	String, type of blast search to perform, e.g. "tblastn" or "blastp"
blast_db	String, path to blast database (you can create a database useing the makeblastdb function)
input	String, path to input query file (sequence to blast against the database)
e	Integer, evalue cutoff to apply, default = 0.01
format	Integer, format type to use for results, default = 6 (tabular). Options: alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = XML Blast output, 6 = tabular, 7 = tabular with comment lines, 8 = Text ASN.1, 9 = Binary ASN.1, 10 = Comma-separated values, 11 = BLAST archive format (ASN.1)

Value

blast_out File with blast results

Examples

## Not run: 
blast(blast = "tblastn",
blast_db = "/home/rstudio/data/tara_db/tara_db",
input = "/home/rstudio/scpackage/inst/extdata/sc_markers.faa",
out = "/home/rstudio/data/test_tara_10n2",
format = 6)

## End(Not run)

uashogeschoolutrecht/structural_colours documentation built on June 20, 2020, 4:07 p.m.