In pmgrollemund/phyloHIV:

options(width = 100)
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Introduction

Purpose of the document

In this document, we describe the options json file that are required for running the example package application in extscript. Below, we firstly deal with options.json file and we secondly describe internal_options.json file that should not be changed.

options

The json file should contain inputs such that:

job_index: an integer that should only corresponds to the array job index, NA otherwise.
path_RDS: path to the folder containing the meta data.
RDS_names: the name of the meta data files.
path_LANL_seq: path to the folder containing the LANL sequences.
LANL_seq_names: the names of the LANL files.
path_local_seq: path to the folder containing the local sequences.
local_seq_names: the names of the local files.
path_aligned: where to store files related to the aligned sequences.
seq_names: the names of the sequence files that will contain the local sequences and the blasted LANL sequences.
path_tree: where to store files related to the trees.
tree_names: the names of the trees
path_colored_tree: where to store files related to the colored trees, as phyloscanner outputs.
path_clades: where to store files related to the extracted subtrees/clades.
local_group: the group name of the local sequences. For instance: "WA" if all of them are from Washington State.
focus_group: which geographical location to focus. For instance: "KC" if King County is the focus.
focus_subgroup: which subgroup to focus. Could be level(s) of a variable in the meta data file. See also "vars_for_label" if you aim to focus on a specific subgroup. For instance: ["HSX_F","HSX_M"].
index_subgroup: the rank of the considered variable (for focus_subgroup) in the tip labels. (This option is tricky to define...).
name_subgroup: a name for defining the subgroup. For instance: "HSX".
bs.n: the bootstrap number.
subtypes: the considered subtype.
verbose: write stuff if true.

You may use the write_option_file function to generate this options json file. See below to generate the same file than which provided as an example.

write_option_file(output_file = "./options.json")

internal options

The json file should contain inputs such that:

nbre_close: the minimum number of closest LANL sequences from each local sequences.
max_closest: the maximum number of closest LANL sequences from each local sequences.
min_percent: the threshold under which we consider that there are not enough LANL sequences.
outgroup_size: the size of the ougroup added to each sequence files.
aligner: the algorithm to use to align the sequence. Keep MAFFT.
thread: MAFFT option.
dna_region: the name of the focused genome region.
nbre_col_rm_strip: the genome location with only n non-gap, where n is lower than nbre_col_rm_strip will be removed.
name_HXB2: the name of the HXB2 sequence.
tree_builder: the algorithm to use to build the tree. Keep fasttree.
local_indicator: the prefix of the local sequence names.
focus_indicator: if true, the subtree will be estimated for a specific group.
separator: a string that will be use to separate the tip name from the group name.
negative: a string for indicating that a tip is not in the focused subgroup.
blacklist_paths: where to store the blacklist files.
blacklist_names: the names of the blacklist files.
Unknown: which group name for those we we do not have an estimated location.
local_tip_split: the string used to separate the information in the local tip names.
external_tip_split: the string used to separate the information in the external/LANL tip names.
local_index_location: the spot of the location in the local tip names.
external_index_location: the spot of the location in the external/LANL tip names.
opt_regex: a regular expression used by phyloscanner. Depends on separator.
vars_for_label: the variables in the meta data that should appear in the local tip names. If you put too much information, you should have a problem to open the newick/fasta file.