-
Notifications
You must be signed in to change notification settings - Fork 4
/
fetch_alphafold_prediction.R
469 lines (445 loc) · 16.9 KB
/
fetch_alphafold_prediction.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
#' Fetch AlphaFold prediction
#'
#' Fetches atom level data for AlphaFold predictions either for selected proteins or whole
#' organisms.
#'
#' @param uniprot_ids optional, a character vector of UniProt identifiers for which predictions
#' should be fetched. This argument is mutually exclusive to the \code{organism_name} argument.
#' @param organism_name optional, a character value providing the name of an organism for which
#' all available AlphaFold predictions should be retreived. The name should be the capitalised
#' scientific species name (e.g. "Homo sapiens"). **Note:** Some organisms contain a lot of
#' predictions which might take a considerable amount of time and memory to fetch. Therefore, you
#' should be sure that your system can handle fetching predictions for these organisms. This
#' argument is mutually exclusive to the \code{uniprot_ids} argument.
#' @param version a character value that specifies the alphafold version that should be used. This
#' is regularly updated by the database. We always try to make the current version the default version.
#' Available version can be found here: https://ftp.ebi.ac.uk/pub/databases/alphafold/
#' @param timeout a numeric value specifying the time in seconds until the download of an organism
#' archive times out. The default is 3600 seconds.
#' @param max_tries a numeric value that specifies the number of times the function tries to download
#' the data in case an error occurs. The default is 5. This only applies if `uniprot_ids` were provided.
#' @param return_data_frame a logical value that specifies if true, a data frame instead of a list
#' is returned. It is recommended to only use this if information for few proteins is retrieved.
#' Default is FALSE.
#' @param show_progress a logical value that specifies if true, a progress bar will be shown.
#' Default is TRUE.
#'
#' @return A list that contains atom level data for AlphaFold predictions. If return_data_frame is
#' TRUE, a data frame with this information is returned instead. The data frame contains the
#' following columns:
#'
#' * label_id: Uniquely identifies every atom in the prediction following the standardised
#' convention for mmCIF files.
#' * type_symbol: The code used to identify the atom species representing this atom type.
#' This code is the element symbol.
#' * label_atom_id: Uniquely identifies every atom for the given residue following the
#' standardised convention for mmCIF files.
#' * label_comp_id: A chemical identifier for the residue. This is the three- letter code
#' for the amino acid.
#' * label_asym_id: Chain identifier following the standardised convention for mmCIF files.
#' Since every prediction only contains one protein this is always "A".
#' * label_seq_id: Uniquely and sequentially identifies residues for each protein. The
#' numbering corresponds to the UniProt amino acid positions.
#' * x: The x coordinate of the atom.
#' * y: The y coordinate of the atom.
#' * z: The z coordinate of the atom.
#' * prediction_score: Contains the prediction score for each residue.
#' * auth_seq_id: Same as \code{label_seq_id}. But of type character.
#' * auth_comp_id: Same as \code{label_comp_id}.
#' * auth_asym_id: Same as \code{label_asym_id}.
#' * uniprot_id: The UniProt identifier of the predicted protein.
#' * score_quality: Score annotations.
#'
#' @import dplyr
#' @import progress
#' @import purrr
#' @import tidyr
#' @importFrom tibble tibble
#' @importFrom utils download.file untar
#' @importFrom readr read_tsv
#' @importFrom stringr str_replace_all str_detect
#' @importFrom curl has_internet
#' @importFrom magrittr %>%
#' @importFrom utils capture.output
#' @export
#'
#' @examples
#' \donttest{
#' alphafold <- fetch_alphafold_prediction(
#' uniprot_ids = c("F4HVG8", "O15552"),
#' return_data_frame = TRUE
#' )
#'
#' head(alphafold, n = 10)
#' }
fetch_alphafold_prediction <- function(uniprot_ids = NULL,
organism_name = NULL,
version = "v4",
timeout = 3600,
max_tries = 5,
return_data_frame = FALSE,
show_progress = TRUE) {
if (!curl::has_internet()) {
message("No internet connection.")
return(invisible(NULL))
}
if (!missing(uniprot_ids) & !missing(organism_name)) {
stop(strwrap("Please only provide either a list of UniProt identifiers or one organism name!",
prefix = "\n", initial = ""
))
}
# if organism name is provided fetch all information about that organism
if (!missing(organism_name)) {
organism_name <- match.arg(organism_name, c(
"Arabidopsis thaliana",
"Caenorhabditis elegans",
"Candida albicans",
"Danio rerio",
"Dictyostelium discoideum",
"Drosophila melanogaster",
"Escherichia coli",
"Glycine max",
"Homo sapiens",
"Leishmania infantum",
"Methanocaldococcus jannaschii",
"Mus musculus",
"Mycobacterium tuberculosis",
"Oryza sativa",
"Plasmodium falciparum",
"Rattus norvegicus",
"Saccharomyces cerevisiae",
"Schizosaccharomyces pombe",
"Staphylococcus aureus",
"Trypanosoma cruzi",
"Zea mays",
"Ajellomyces capsulatus",
"Brugia malayi",
"Campylobacter jejuni",
"Cladophialophora carrionii",
"Dracunculus medinensis",
"Enterococcus faecium",
"Fonsecaea pedrosoi",
"Haemophilus influenzae",
"Helicobacter pylori",
"Klebsiella pneumoniae",
"Leishmania infantum",
"Madurella mycetomatis",
"Mycobacterium leprae",
"Mycobacterium tuberculosis",
"Mycobacterium ulcerans",
"Neisseria gonorrhoeae",
"Nocardia brasiliensis",
"Onchocerca volvulus",
"Paracoccidioides lutzii",
"Plasmodium falciparum",
"Pseudomonas aeruginosa",
"Salmonella typhimurium",
"Schistosoma mansoni",
"Shigella dysenteriae",
"Sporothrix schenckii",
"Staphylococcus aureus",
"Streptococcus pneumoniae",
"Strongyloides stercoralis",
"Trichuris trichiura",
"Trypanosoma brucei",
"Trypanosoma cruzi",
"Wuchereria bancrofti"
))
organism_file <- switch(organism_name,
"Arabidopsis thaliana" = "UP000006548_3702_ARATH",
"Caenorhabditis elegans" = "UP000001940_6239_CAEEL",
"Candida albicans" = "UP000000559_237561_CANAL",
"Danio rerio" = "UP000000437_7955_DANRE",
"Dictyostelium discoideum" = "UP000002195_44689_DICDI",
"Drosophila melanogaster" = "UP000000803_7227_DROME",
"Escherichia coli" = "UP000000625_83333_ECOLI",
"Glycine max" = "UP000008827_3847_SOYBN",
"Homo sapiens" = "UP000005640_9606_HUMAN",
"Leishmania infantum" = "UP000008153_5671_LEIIN",
"Methanocaldococcus jannaschii" = "UP000000805_243232_METJA",
"Mus musculus" = "UP000000589_10090_MOUSE",
"Mycobacterium tuberculosis" = "UP000001584_83332_MYCTU",
"Oryza sativa" = "UP000059680_39947_ORYSJ",
"Plasmodium falciparum" = "UP000001450_36329_PLAF7",
"Rattus norvegicus" = "UP000002494_10116_RAT",
"Saccharomyces cerevisiae" = "UP000002311_559292_YEAST",
"Schizosaccharomyces pombe" = "UP000002485_284812_SCHPO",
"Staphylococcus aureus" = "UP000008816_93061_STAA8",
"Trypanosoma cruzi" = "UP000002296_353153_TRYCC",
"Zea mays" = "UP000007305_4577_MAIZE",
"Ajellomyces capsulatus" = "UP000001631_447093_AJECG",
"Brugia malayi" = "UP000006672_6279_BRUMA",
"Campylobacter jejuni" = "UP000000799_192222_CAMJE",
"Cladophialophora carrionii" = "UP000094526_86049_9EURO1",
"Dracunculus medinensis" = "UP000274756_318479_DRAME",
"Enterococcus faecium" = "UP000325664_1352_ENTFC",
"Fonsecaea pedrosoi" = "UP000053029_1442368_9EURO2",
"Haemophilus influenzae" = "UP000000579_71421_HAEIN",
"Helicobacter pylori" = "UP000000429_85962_HELPY",
"Klebsiella pneumoniae" = "UP000007841_1125630_KLEPH",
"Leishmania infantum" = "UP000008153_5671_LEIIN",
"Madurella mycetomatis" = "UP000078237_100816_9PEZI1",
"Mycobacterium leprae" = "UP000000806_272631_MYCLE",
"Mycobacterium tuberculosis" = "UP000001584_83332_MYCTU",
"Mycobacterium ulcerans" = "UP000020681_1299332_MYCUL",
"Neisseria gonorrhoeae" = "UP000000535_242231_NEIG1",
"Nocardia brasiliensis" = "UP000006304_1133849_9NOCA1",
"Onchocerca volvulus" = "UP000024404_6282_ONCVO",
"Paracoccidioides lutzii" = "UP000002059_502779_PARBA",
"Plasmodium falciparum" = "UP000001450_36329_PLAF7",
"Pseudomonas aeruginosa" = "UP000002438_208964_PSEAE",
"Salmonella typhimurium" = "UP000001014_99287_SALTY",
"Schistosoma mansoni" = "UP000008854_6183_SCHMA",
"Shigella dysenteriae" = "UP000002716_300267_SHIDS",
"Sporothrix schenckii" = "UP000018087_1391915_SPOS1",
"Staphylococcus aureus" = "UP000008816_93061_STAA8",
"Streptococcus pneumoniae" = "UP000000586_171101_STRR6",
"Strongyloides stercoralis" = "UP000035681_6248_STRER",
"Trichuris trichiura" = "UP000030665_36087_TRITR",
"Trypanosoma brucei" = "UP000008524_185431_TRYB2",
"Trypanosoma cruzi" = "UP000002296_353153_TRYCC",
"Wuchereria bancrofti" = "UP000270924_6293_WUCBA"
)
url <- paste0("https://ftp.ebi.ac.uk/pub/databases/alphafold/", version, "/", organism_file, "_", version, ".tar")
# set new longer timeout and reset to standard once function exits.
old <- options(timeout = timeout)
on.exit(options(old))
# This does not fail gracefully. I could not figure out how to
# catch the error and the two warnings in case of a timeout.
# The error would not be caught while only the first warning that does not
# contain the timeout information was caught.
utils::download.file(url, destfile = paste0(tempdir(), "/alphafold.tar"))
utils::untar(
tarfile = paste0(tempdir(), "/alphafold.tar"),
exdir = paste0(tempdir(), "/alphafold")
)
all_files <- paste0(
tempdir(),
"/alphafold/",
list.files(
path = paste0(
tempdir(),
"/alphafold"
),
pattern = ".cif.gz"
)
)
all_protein_ids <- str_extract(all_files,
pattern = "(?<=AF-).+(?=-F1)"
)
names(all_files) <- all_protein_ids
if (show_progress == TRUE) {
pb <- progress::progress_bar$new(
total = length(all_files),
format = paste0(
"Importing AlphaFold predictions for ",
organism_name,
"[:bar] :current/:total (:percent) :eta"
)
)
}
query_result <- purrr::map(
.x = all_files,
.f = ~ {
if (show_progress == TRUE) {
pb$tick()
}
readr::read_tsv(.x, col_names = FALSE, quote = "", show_col_types = FALSE, progress = FALSE) %>%
dplyr::filter(stringr::str_detect(X1, pattern = "^ATOM\\s+\\d|^HETATM\\s+\\d")) %>%
dplyr::mutate(X2 = stringr::str_replace_all(X1, pattern = "\\s+", replacement = " ")) %>%
tidyr::separate(X2,
sep = " ",
into = c(
"x1",
"label_id",
"type_symbol",
"label_atom_id",
"x2",
"label_comp_id",
"label_asym_id",
"entity_id",
"label_seq_id",
"x3",
"x",
"y",
"z",
"site_occupancy",
"prediction_score",
"formal_charge",
"auth_seq_id",
"auth_comp_id",
"auth_asym_id",
"x4",
"pdb_model_number",
"uniprot_id",
"x5",
"x6",
"x7"
)
) %>%
dplyr::select(-c(
"X1",
"x1",
"x2",
"x3",
"x4",
"x5",
"x6",
"x7",
"formal_charge",
"site_occupancy",
"entity_id",
"pdb_model_number"
)) %>%
dplyr::mutate(
label_id = as.numeric(.data$label_id),
label_seq_id = as.numeric(.data$label_seq_id),
x = as.numeric(.data$x),
y = as.numeric(.data$y),
z = as.numeric(.data$z),
prediction_score = as.numeric(.data$prediction_score),
auth_seq_id = .data$auth_seq_id
) %>%
dplyr::mutate(score_quality = dplyr::case_when(
.data$prediction_score > 90 ~ "very_good",
.data$prediction_score > 70 ~ "confident",
.data$prediction_score > 50 ~ "low",
.data$prediction_score <= 50 ~ "very_low"
))
}
)
# delete files after everything is done
unlink(paste0(tempdir(), "/alphafold"), recursive = TRUE)
unlink(paste0(tempdir(), "/alphafold.tar"))
} else {
# remove NAs from UniProt IDs
uniprot_ids <- uniprot_ids[!is.na(uniprot_ids)]
batches <- purrr::map(
.x = uniprot_ids,
.f = ~ paste0("https://alphafold.ebi.ac.uk/files/AF-", .x, "-F1-model_", version, ".cif")
)
names(batches) <- uniprot_ids
if (show_progress == TRUE) {
pb <- progress::progress_bar$new(
total = length(batches),
format = " Fetching AlphaFold predictions [:bar] :current/:total (:percent) :eta"
)
}
query_result <- purrr::map(
.x = batches,
.f = ~ {
# query information from database
query <- try_query(.x,
type = "text/tab-separated-values",
timeout = timeout,
max_tries = max_tries,
col_names = FALSE,
quote = "",
show_col_types = FALSE,
progress = FALSE
)
if (show_progress == TRUE) {
pb$tick()
}
# only proceed with data if it was correctly retrieved
if ("tbl" %in% class(query)) {
query %>%
dplyr::filter(stringr::str_detect(X1, pattern = "^ATOM\\s+\\d|^HETATM\\s+\\d")) %>%
dplyr::mutate(X2 = stringr::str_replace_all(X1, pattern = "\\s+", replacement = " ")) %>%
tidyr::separate(X2,
sep = " ",
into = c(
"x1",
"label_id",
"type_symbol",
"label_atom_id",
"x2",
"label_comp_id",
"label_asym_id",
"entity_id",
"label_seq_id",
"x3",
"x",
"y",
"z",
"site_occupancy",
"prediction_score",
"formal_charge",
"auth_seq_id",
"auth_comp_id",
"auth_asym_id",
"x4",
"pdb_model_number",
"uniprot_id",
"x5",
"x6",
"x7"
)
) %>%
dplyr::select(-c(
"X1",
"x1",
"x2",
"x3",
"x4",
"x5",
"x6",
"x7",
"formal_charge",
"site_occupancy",
"entity_id",
"pdb_model_number"
)) %>%
dplyr::mutate(
label_id = as.numeric(.data$label_id),
label_seq_id = as.numeric(.data$label_seq_id),
x = as.numeric(.data$x),
y = as.numeric(.data$y),
z = as.numeric(.data$z),
prediction_score = as.numeric(.data$prediction_score),
auth_seq_id = .data$auth_seq_id
) %>%
dplyr::mutate(score_quality = dplyr::case_when(
.data$prediction_score > 90 ~ "very_good",
.data$prediction_score > 70 ~ "confident",
.data$prediction_score > 50 ~ "low",
.data$prediction_score <= 50 ~ "very_low"
))
} else {
query
}
}
)
}
# catch any IDs that have not been fetched correctly
error_list <- query_result %>%
purrr::keep(.p = ~ is.character(.x))
if (length(error_list) != 0) {
error_table <- tibble::tibble(
id = names(error_list),
error = unlist(error_list)
) %>%
dplyr::distinct()
if (any(stringr::str_detect(unique(error_table$error), pattern = "Timeout"))) {
message('The retrieval of data timed out. Consider increasing the "timeout" or "max_tries" argument. \n')
}
message("The following IDs have not been retrieved correctly.")
message(paste0(utils::capture.output(error_table), collapse = "\n"))
}
# only keep data in output
query_result <- query_result %>%
purrr::keep(.p = ~ !is.character(.x))
if (length(query_result) == 0) {
message("No valid information could be retrieved!")
return(invisible(NULL))
}
if (return_data_frame == FALSE) {
return(query_result)
} else {
query_result_df <- purrr::map_dfr(
.x = query_result,
.f = ~.x
)
return(query_result_df)
}
}