readBlastOutput | R Documentation |
Wrapper functions to implement a call to BLAST, and turn the results of a BLAST query into an R table.
callBlast( fastafile, outfile = "blastOut.txt", program = "blastn", db = "nt",
path = Sys.getenv("BLASTINDEX_PATH"), task = "", wordsize = 8, evalue = 1,
threads = 4, outfmt = 6, filter = "no", maxhits = 5, blastArgs = "")
callBlastn( fastafile, outfile = "blastOut.txt", program = "blastn", db = "NT/nt",
path = Sys.getenv("BLASTINDEX_PATH"), task = "", wordsize = 8, evalue = 1,
threads = 4, outfmt = 6, filter = "no", maxhits = 5, blastArgs = "")
callBlastp( fastafile, outfile = "blastOut.txt", program = "blastp", db = "NR/nr",
path = Sys.getenv("BLASTINDEX_PATH"), task = "", wordsize = 3, evalue = 1,
threads = 4, outfmt = 6, filter = "no", maxhits = 5, blastArgs = "")
readBlastOutput( infile, outfmt = 6, verbose = TRUE, nKeep = NULL)
fastafile |
Character string, full pathname to an existing FASTA file of query sequences to submit to BLAST. |
outfile |
Character string, full pathname for the resulting output from BLAST. |
program |
Character string, full pathname for the executable version of BLAST. Passed to |
db |
Character string, name of the BLAST database to search against. |
path |
Character string, full pathname to the folder containing the BLAST database files. |
outfmt |
Blast output mode. Currently, only |
infile |
Character string, full pathname to an existing file created by BLAST using output mode '-outfmt=6'. |
nKeep |
When NULL, keep all BLAST hits for each query sequence, else an integer specifying the maximum number of
BLAST matches to return for each query. Only the highest scoring |
The BLAST command line details and result format assume a BLAST version of at least 2.2.25
For the calls to BLAST, no return value, just a file of results written to disk.
For reaedBlastOutput
, a data frame with columns:
PROBE_ID, SEQ_ID, PCT_MATCH, LEN_MATCH, MIS_MATCH, GAP,
P_FIRST, P_LAST, S_BEG, S_END, E_VALUE, SCORE, STRAND
that contains the BLAST results from the file.
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