In some cases, users may wish to extract the sequences of the respective blast hit stored in a blast_tbl. This function enables to quickly extract such sequences and store them in one general or multiple genome specific fasta file(s).

extract_hit_seqs_from_genomes(
  blast_tbl,
  subject_genomes,
  file_name = NULL,
  separated_by_genome = FALSE,
  update = TRUE,
  path = NULL
)

Arguments

blast_tbl

a BLAST table generated with blast_genomes.

subject_genomes

a vector containing file paths to the reference genomes that shall be queried (e.g. file paths returned by meta.retrieval).

file_name

name of the fasta file that stores the BLAST hit sequences. This name will only be used when separated_by_genome = FALSE.

separated_by_genome

a logical value indicating whether or not hit sequences from different genomes should be stored in the same output fasta file separated_by_genome = FALSE (default) or in separate fasta files separated_by_genome = TRUE.

update

shall an existing file_name file be overwritten (update = TRUE; Default) or shall blast hit sequences be appended to the existing file (update = FALSE)?

path

a folder path in which corresponding fasta output files shall be stored.