write_option_file: write_option_file

In pmgrollemund/phyloHIV:

Description

Extract the HXB2 sequence from a LANL dataset.

Usage

write_option_file(output_file = "./options.json",
  path_RDS = "./extdata/FakeData/",
  RDS_names = c("sequences_meta_modified.rds", "person_modified.rds",
  "Country_db.rds"), path_LANL_seq = "./extdata/LANL/",
  LANL_seq_names = c("LANL_Subtype_01_AE_stripped.fasta",
  "LANL_Subtype_A1_stripped.fasta"), path_seq = "./extdata/Subtype/",
  seq_names = c("newseq_Subtype_01_AE.fasta", "newseq_Subtype_A1.fasta"),
  path_file_aligned = "./extdata/Closest/",
  names_file_aligned = c("newseq_LANL_Subtype_01_AE",
  "newseq_LANL_Subtype_A1"), path_tree = "./extdata/Tree/",
  tree_names = c("newseq_LANL_Subtype_01_AE_mafft_aligned_ndrm",
  "newseq_LANL_Subtype_A1_mafft_aligned_ndrm"),
  path_colored_tree = "./extdata/Colored_tree/",
  path_clades = "./extdata/Clades/", local_group = "WA",
  focus_group = "KC", focus_subgroup = "null",
  index_subgroup = "null", name_subgroup = "null", bs.n = 2,
  subtypes = c("01_AE", "A1"), job_index = NA, verbose = "true")

Arguments

output_file	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
path_RDS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
RDS_names	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
path_LANL_seq	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
LANL_seq_names	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
path_seq	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
seq_names	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
path_file_aligned	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
names_file_aligned	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
path_tree	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
tree_names	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
path_colored_tree	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
path_clades	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
local_group	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
focus_group	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
focus_subgroup	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
index_subgroup	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
name_subgroup	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
bs.n	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
subtypes	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
job_index	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx
verbose	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXx

Value

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pmgrollemund/phyloHIV documentation built on Nov. 5, 2019, 12:56 a.m.