blastTranscriptomes: BLAST search local transcriptomes

In LucasBusta/phyloChemistry: Chemical and Sequence Analyses in a Phylogenetic Context

Description

Search locally stored transcriptomes for query sequences.

Usage

blastTranscriptomes(transcriptomes, query_in_path,
  sequences_of_interest_directory_path, blast_module_directory_path,
  blast_type = c("blastn", "dc-megablast"), remove = NULL,
  monolist_out_path)

Arguments

transcriptomes	A list of paths to the transcriptomes that should be searched, named by taxonomic identifier (e.g. species names)
query_in_path	Path to a fasta file containing the query
sequences_of_interest_directory_path	Path to a directory where blast hits should be written out as fasta files
blast_type	One of "blastn" or "dc-megablast"
remove	Names of columns to remove from the output monolist
monolist_out_path	Path to where the output monolist should be written

LucasBusta/phyloChemistry documentation built on Sept. 6, 2020, 11:36 p.m.