run_blastdbcmd_blastn_and_aggregate_resuts {rCRUX} | R Documentation |
run_blastdbcmd()
, run_blastn()
, and aggregates and
saves the resultsIt uses run_blastdbcmd()
to find a seed sequence that corresponds to
the accession number and forward and reverse stops recorded in the seeds table.
run_blastdbcmd()
outputs sequences as .fasta-formatted strings, which
run_blastdbcmd_blastn_and_aggregate_resuts concatenates into a multi-line
fasta, then passes to run_blastn()
as an argument. The output of
run_blastn()
is de-replicated by accession, and only the longest
read per replicates is retained in the output table. The run state is saved
and passed back to blast_datatable()
.
run_blastdbcmd_blastn_and_aggregate_resuts(
sample_indices = sample_indices,
save_dir,
blast_seeds_m,
ncbi_bin = NULL,
db,
too_many_ns,
db_dir,
blastdbcmd_failed,
unsampled_indices,
output_table,
wildcards,
num_rounds,
...
)
sample_indices |
the indices to sample |
save_dir |
a directory in which to create files representing the current state |
blast_seeds_m |
blast seeds table but with blast status update |
ncbi_bin |
passed to |
db |
the type of blast db - e.g. nt |
too_many_ns |
a vector of indices that result in a fasta with too many Ns |
db_dir |
path to the blast db |
blastdbcmd_failed |
the indicies not found in your blast db |
unsampled_indices |
the indices that need to be sampled |
output_table |
the table of results |
wildcards |
is a character vector that represents the minimum number of consecutive Ns the user will tolerate in a given seed or hit sequence. The default is wildcards = "NNNN" |
num_rounds |
number of rounds of blast |
... |
additional arguments passed to |