loadBlast: BLAST

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

BLAST

Description

Load alignment coordinates from the NCBI BLAST.

Usage

loadBlast(
  file.coords,
  reformat.strand = TRUE,
  apply.sort = TRUE,
  asGRanges = TRUE,
  verbose = 1
)

Arguments

file.coords	path to the file with alignment coordinates obtained with -outfmt "6 std qlen sstrand"
reformat.strand	if TRUE, "plus" is replaced by "+", and "minus" by "-"
apply.sort	if TRUE, return the alignments sorted in increasing order for qseqid, then increasing for evalue, then decreasing for bitscore, then decreasing for length, then decreasing for pident, then increasing for sseqid
asGRanges	if TRUE, returns a GRanges object
verbose	verbosity level (0/1)

Value

GRanges or data.frame with 14 columns

Author(s)

Timothee Flutre

See Also

blast2granges

Examples

## Not run: ## BLAST should be run beforehand, for instance:
## zcat chroms.fa.gz | makeblastdb -dbtype nucl -in - -title chroms -out chroms -logfile makeblastdb_chroms.log
## echo "zcat seqs.fa.gz | blastn -query - -task megablast -db chroms -out /dev/stdout -outfmt \"6 std qlen sstrand\" | gzip > megablast_chroms_seqs.txt.gz"  | qsub ...
coords <- loadBlast("megablast_chroms_seqs.txt.gz")

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.