Description Usage Arguments Value
View source: R/other_functions.R
Extract the HXB2 sequence from a LANL dataset.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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")
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output_file |
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path_RDS |
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RDS_names |
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path_LANL_seq |
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LANL_seq_names |
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path_seq |
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seq_names |
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path_file_aligned |
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names_file_aligned |
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path_tree |
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tree_names |
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path_colored_tree |
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path_clades |
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local_group |
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focus_group |
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focus_subgroup |
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index_subgroup |
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name_subgroup |
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bs.n |
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subtypes |
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job_index |
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verbose |
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