readBlastTable: Reading BLAST result file

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/blasting.R

Description

Reading a file produced by the BLAST+ software set up to produce tabular output.

Usage

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readBlastTable(blast.file)

Arguments

blast.file

Name of file to read.

Details

This function will read files produced by the BLAST+ software where the option -outfmt 6 has been invoked during its call. This option forces BLAST to produce a short tabular text output for each BLAST search. The function blastAllAll produces such files.

Value

The content of the file is returned as a data.frame with 12 columns and one row for each BLAST result. The columns have self-explanatory names.

Author(s)

Lars Snipen and Kristian Hovde Liland.

See Also

blastAllAll, bDist.

Examples

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# Using a BLAST result file in this package
xpth <- file.path(path.package("micropan"),"extdata")
blast.file <- file.path( xpth, "GID1_vs_GID2.txt.xz" )

# We need to uncompress it first...
tf <- tempfile(fileext=".xz")
s <- file.copy(blast.file,tf)
tf <- xzuncompress(tf)

#...then we can read it...
blast.table <- readBlastTable(tf)

# ...and deleting temporary file
s <- file.remove(tf)

micropan documentation built on Feb. 15, 2018, 5 p.m.