@@ -13,32 +13,37 @@ utils::globalVariables(".data")
1313# ' @param force Logical; by default (`FALSE`), .mol files will not be downloaded
1414# ' if they are found in `dir`. Set this to `TRUE` to download and overwrite
1515# ' existing files.
16- # '
16+ # '
17+ # ' @note For additional functionality for interacting with KEGG, try the
18+ # ' `KEGGREST` package, which this function was inspired by.
19+ # '
1720# ' @returns A tibble with the columns `compound_ids`, `pathway_ids` (if used),
1821# ' and `mol_paths` (paths to downloaded .mol files).
22+ # '
1923# ' @export
2024# '
2125# ' @examples
2226# ' \dontrun{
2327# ' get_mol_kegg(compound_ids = c("C16181", "C06074"), dir = tempdir())
2428# ' get_mol_kegg(pathway_ids = "map00253", dir = tempdir())
2529# ' }
26- get_mol_kegg <- function (compound_ids , pathway_ids , dir , force = FALSE ){
27-
28- if (missing(dir )) stop(" `dir` is required"
29- if ((missing(compound_ids ) & missing(pathway_ids )) |
30- ! missing(compound_ids ) & ! missing(pathway_ids )) {
30+ get_mol_kegg <- function (compound_ids , pathway_ids , dir , force = FALSE ) {
31+ if (missing(dir )) stop(" `dir` is required"
32+ if (
33+ (missing(compound_ids ) & missing(pathway_ids )) |
34+ ! missing(compound_ids ) & ! missing(pathway_ids )
35+ ) {
3136 stop(" One of `compound_ids` or `pathway_ids` are required"
3237 }
33-
38+
3439 # if compounds are provided
3540 if (! missing(compound_ids )) {
3641 if (! all(stringr :: str_detect(compound_ids , " ^[C][:digit:]{5}$"
3742 stop(" Some compound_ids are not in the correct KEGG format"
3843 }
3944 fs :: dir_create(dir )
4045 out_tbl <-
41- tibble :: tibble(compound_id = compound_ids ) %> %
46+ tibble :: tibble(compound_id = compound_ids ) %> %
4247 dplyr :: mutate(mol_path = fs :: path(dir , .data $ compound_id , ext = " mol"
4348 }
4449 # if pathways are provided
@@ -47,30 +52,40 @@ get_mol_kegg <- function(compound_ids, pathway_ids, dir, force = FALSE){
4752 stop(" Some pathway_ids are not in the correct KEGG format"
4853 }
4954 fs :: dir_create(dir , pathway_ids )
50- compound_ids_list <- lapply(pathway_ids , keggGetCompounds )
55+ compound_ids_list <- lapply(pathway_ids , get_compounds_kegg )
5156 names(compound_ids_list ) <- pathway_ids
52- out_tbl <-
53- tibble :: enframe(compound_ids_list , name = " pathway_id" value = " compound_id" > %
54- tidyr :: unnest(tidyselect :: everything()) %> %
55- dplyr :: mutate(mol_path = fs :: path(dir , .data $ pathway_id , .data $ compound_id , ext = " mol"
57+ out_tbl <-
58+ tibble :: enframe(
59+ compound_ids_list ,
60+ name = " pathway_id"
61+ value = " compound_id"
62+ ) %> %
63+ tidyr :: unnest(tidyselect :: everything()) %> %
64+ dplyr :: mutate(
65+ mol_path = fs :: path(
66+ dir ,
67+ .data $ pathway_id ,
68+ .data $ compound_id ,
69+ ext = " mol"
70+ )
71+ )
5672 }
57-
58- if (isFALSE(force )) {
73+
74+ if (isFALSE(force )) {
5975 to_dl <- out_tbl $ compound_id [! fs :: file_exists(out_tbl $ mol_path )]
6076 out_paths <- out_tbl $ mol_path [! fs :: file_exists(out_tbl $ mol_path )]
6177 } else {
6278 to_dl <- out_tbl $ compound_id
6379 out_paths <- out_tbl $ mol_path
6480 }
65-
81+
6682 if (length(to_dl ) == 0 ) {
6783 # if nothing to download, return early
6884 return (out_tbl )
6985 } else {
70-
7186 # Download mols
7287 mols <- dl_mol_kegg(to_dl )
73-
88+
7489 # write mol files
7590 .write_mol <- function (mol_clean , file_path ) {
7691 utils :: write.table(
@@ -81,76 +96,98 @@ get_mol_kegg <- function(compound_ids, pathway_ids, dir, force = FALSE){
8196 quote = FALSE
8297 )
8398 }
84-
99+
85100 mapply(.write_mol , mol_clean = mols , file_path = out_paths )
86-
101+
87102 return (out_tbl )
88103 }
89104}
90105
91106
92107# ' Get list of KEGG compound IDs for given KEGG pathway
93108# '
94- # ' This is a temporary helper function until this function is improved and
95- # ' pushed into KEGGREST package
96- # '
97109# ' @param pathway string that is a KEGG identifier for a molecular pathway
98110# ' @noRd
99- keggGetCompounds <- function (pathway ){
100-
101- resp <-
102- httr2 :: request(" https://rest.kegg.jp/" > %
103- httr2 :: req_url_path(" link/cpd/" > %
104- httr2 :: req_url_path_append(pathway ) %> %
105- httr2 :: req_retry(max_tries = 3 ) %> %
111+ get_compounds_kegg <- function (pathway ) {
112+ resp <-
113+ httr2 :: request(" https://rest.kegg.jp/" > %
114+ httr2 :: req_user_agent(
115+ " volcalc (https://github.com/Meredith-Lab/volcalc/)"
116+ ) %> %
117+ httr2 :: req_url_path(" link/cpd/" > %
118+ httr2 :: req_url_path_append(pathway ) %> %
119+ httr2 :: req_retry(max_tries = 3 ) %> %
106120 httr2 :: req_perform()
107-
108- out <- resp %> %
109- httr2 :: resp_body_string() %> %
110- stringr :: str_split_1(" \n " > %
121+
122+ out <- resp %> %
123+ httr2 :: resp_body_string() %> %
124+ stringr :: str_split_1(" \n " > %
111125 stringr :: str_extract(" (?<=cpd:).*"
112126 out [! is.na(out )]
113-
114127}
115128
116- dl_mol_kegg <- function (compound_ids ) {
117- # balances compound_ids into groups of less than 10 to meet API guidelines
118- compound_id_list <- split_to_list(compound_ids , max_len = 10 )
119-
120- # maps over list, but returns it to a single character vector to simplify wrangling code
121- raw <-
122- purrr :: map(compound_id_list , function (x ) KEGGREST :: keggGet(x , option = " mol" > %
123- purrr :: list_c() %> %
124- glue :: glue_collapse()
125- # split into multiples
126- mols <- stringr :: str_split(raw , " (?<=\\ ${4})" n = length(compound_ids )) %> %
127- unlist() %> %
128- stringr :: str_trim(side = " left"
129-
130- # Adds title to mol file because it is used later on by get_fx_groups()
131- titles <- purrr :: map(compound_id_list , function (x ) { # for every group of <10 IDs
132- KEGGREST :: keggGet(x ) %> %
133- purrr :: map_chr(function (names ) { # for every ID
134- purrr :: pluck(names , " NAME" 1 ) %> % # get first element of NAME
135- stringr :: str_remove(" ;"
136- })
137- }) %> % unlist()
138- purrr :: map2(mols , titles , function (mol , title ) {
139- paste0(title , " \n\n\n " " >.*" " " mol ))
140- })
141-
142- }
129+ # ' Get and wrangle mol files for a single API request of up to 10 IDs
130+ # ' @noRd
131+ .dl_mol_kegg <- function (ids ) {
132+ if (length(ids ) > 10 ) {
133+ stop(" Provide 10 or fewer IDs at a time"
134+ }
135+ req_names <-
136+ httr2 :: request(" https://rest.kegg.jp/get" > %
137+ httr2 :: req_user_agent(
138+ " volcalc (https://github.com/Meredith-Lab/volcalc/)"
139+ ) %> %
140+ httr2 :: req_url_path_append(paste(ids , collapse = " +" > %
141+ httr2 :: req_retry(max_tries = 3 )
142+
143+ resp_names <- httr2 :: req_perform(req_names ) %> %
144+ httr2 :: resp_body_string()
145+
146+ # There's a lot of stuff in the response, but I only care about the compound name
147+ names <- resp_names %> %
148+ stringr :: str_extract_all(" (?<=NAME).+(?=\\ n)" > %
149+ unlist() %> %
150+ stringr :: str_trim() %> %
151+ stringr :: str_remove(" ;"
143152
153+ # get mol file
154+ req_mols <- req_names %> %
155+ httr2 :: req_url_path_append(" mol"
144156
157+ resp_mols <- httr2 :: req_perform(req_mols ) %> %
158+ httr2 :: resp_body_string()
159+
160+ # wrangle into valid mol files
161+ mols <- resp_mols %> %
162+ stringr :: str_split(" (?<=\\ ${4})" n = length(ids )) %> %
163+ unlist() %> %
164+ stringr :: str_trim(side = " left"
165+ mols <-
166+ gsub(" >.*" " " mols ) # for some reason this pattern doesn't work with str_remove()
167+
168+ # add compound name in correct place
169+ paste0(names , " \n\n\n " mols )
170+ }
145171
172+ # ' Split vector into list elements of max length
173+ # ' @noRd
146174split_to_list <- function (x , max_len = 10 ) {
147-
148- if (length(x ) > max_len ) {
175+ if (length(x ) > max_len ) {
149176 n_groups <- ceiling(length(x ) / max_len )
150177 split(x , f = cut(seq_along(x ), breaks = n_groups )) %> %
151178 purrr :: set_names(NULL )
152179 } else {
153180 list (x )
154181 }
155-
182+ }
183+
184+ # ' Get mol files for compound_ids by splitting into groups of 10 and calling .dl_mol_kegg
185+ # ' @noRd
186+ dl_mol_kegg <- function (compound_ids ) {
187+ # balances compound_ids into groups of less than 10 to meet API guidelines
188+ compound_id_list <- split_to_list(compound_ids , max_len = 10 )
189+
190+ # maps over list, but returns it to a single character vector to simplify wrangling code
191+ purrr :: map(compound_id_list , .dl_mol_kegg , .progress = " Downloading" > %
192+ purrr :: list_c()
156193}
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