Reading a file produced by the BLAST+ software set up to produce tabular output.
Name of file to read.
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.
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.
Lars Snipen and Kristian Hovde Liland.
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# Using a BLAST result file in this package # We need to uncompress it first... extdata.path <- file.path(path.package("micropan"),"extdata") filenames <- "GID1_vs_GID2.txt" pth <- lapply( file.path( extdata.path, paste( filenames, ".xz", sep="" ) ), xzuncompress ) #...then we can read it... blast.table <- readBlastTable(file.path(extdata.path,filenames)) # ...and compressing it again... pth <- lapply( file.path( extdata.path, filenames ), xzcompress )