Initialize a new project database

Initialize a new project database

Usage

new_db_userAsmb(
  db_path = "./.sqlite",
  mapping_fn = NULL,
  mapping_id = "ID",
  mapping_taxon = "Taxon",
  genetic_code = 2,
  annotate_cpus = 6,
  annotate_memory = 36,
  annotate_ref_db = "Chordata",
  annotate_ref_dir = "/ref_dbs/Mitos2",
  mitos_opts = "--intron 0 --oril 0",
  trnaScan_opts = "-M vert",
  curate_cpus = 4,
  curate_memory = 8,
  curate_target = "fish_mito",
  max_blast_hits = 100,
  curate_params = NULL
)

Arguments

db_path

Path to the new database file

mapping_fn

Path to the mapping CSV file. Must contain columns "ID", "Taxon, "R1", and "R2"

mapping_id

Column name of the mapping file to use as the primary key

mapping_taxon

Column name of the mapping file containing a Taxonomic identifier (eg, species name)

genetic_code

Translation table for your organisms. See NCBI website for more info https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

annotate_cpus

Default # cpus for annotation

annotate_memory

Default memory (GB) for annotation

annotate_ref_db

Default Mitos2 reference database

annotate_ref_dir

Default Mitos2 reference database directory

mitos_opts

Default MITOS2 command line options

trnaScan_opts

Default tRNAscan-SE command line options

curate_cpus

Default # cpus for curation

curate_memory

Default memory (GB) for curation

curate_target

Default target database for curation

max_blast_hits

Maximum number of top BLAST hits to retain (default = 100)

curate_params

Default curation parameters