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
|
### =========================================================================
### Read a mask from a file
### -----------------------
###
### From an NCBI "agp" file (for chrY in hs b36v3):
### library(BSgenome.Hsapiens.NCBI.b36v3)
### file1 <- system.file("extdata", "hs_b36v3_chrY.agp", package="IRanges")
### mask1 <- read.agpMask(file1, seqname="chrY", mask.width=length(Hsapiens$chrY))
###
### From an UCSC "gap" file (for chrY in hg18):
### library(BSgenome.Hsapiens.UCSC.hg18)
### file2 <- system.file("extdata", "chrY_gap.txt", package="IRanges")
### mask2 <- read.gapMask(file2, seqname="chrY", mask.width=length(Hsapiens$chrY))
###
### From an UCSC "lift" file (for hg18):
### file3 <- system.file("extdata", "hg18liftAll.lft", package="IRanges")
### mask3 <- read.liftMask(file3, seqname="chr1")
###
### From a RepeatMasker .out file (for chrM in ce2):
### library(BSgenome.Celegans.UCSC.ce2)
### file4 <- system.file("extdata", "ce2chrM.fa.out", package="IRanges")
### mask4 <- read.rmMask(file4, seqname="chrM", mask.width=length(Celegans$chrM))
###
### From a Tandem Repeats Finder .bed file (for chrM in ce2):
### file5 <- system.file("extdata", "ce2chrM.bed", package="IRanges")
### mask5 <- read.trfMask(file5, seqname="chrM", mask.width=length(Celegans$chrM))
###
### -------------------------------------------------------------------------
.showDistinctSeqnamesAndStop <- function(seqnames)
{
distinct_seqnames <- paste("\"", unique(seqnames), "\"", sep="")
distinct_seqnames <- paste(distinct_seqnames, collapse=", ")
stop(length(distinct_seqnames), " distinct seqnames found in this file: ", distinct_seqnames)
}
.newEmptyMask <- function(seqname, mask.width, mask.name, mask.desc, nofound_what="information")
{
msg <- paste("No ", nofound_what, " found for sequence \"",
seqname, "\" in this file. ", sep="")
if (is.na(mask.width))
stop(msg, "Please use the\n",
" 'mask.width' argument to specify the width of the empty mask to\n",
" return (i.e. the length of the sequence this mask will be put on).")
warning(msg, "returning empty mask")
ans <- Mask(mask.width) # empty mask
names(ans) <- mask.name
desc(ans) <- paste(mask.desc, "(empty)")
ans
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### read.agpMask() and read.gapMask() extract the AGAPS mask from an NCBI
### "agp" file or a UCSC "gap" file, respectively.
###
.guessGapFileCOL2CLASS <- function(file)
{
## UCSC "gap" files generally have the 9 columns below except for some
## organisms like Rhesus that have only 8 columns (no 'bin' column).
COL2CLASS <- c(
`bin`="integer",
`chrom`="character",
`chr_start`="integer",
`chr_stop`="integer",
`part_no`="integer",
`part_type`="character",
`gap_len`="integer",
`gap_type`="character",
`bridge`="character"
)
line1 <- try(read.table(file, sep="\t",
col.names=names(COL2CLASS),
colClasses=COL2CLASS,
nrows=1L,
check.names=FALSE),
silent=TRUE)
if (!inherits(line1, "try-error"))
return(COL2CLASS)
COL2CLASS <- COL2CLASS[-1L]
line1 <- try(read.table(file, sep="\t",
col.names=names(COL2CLASS),
colClasses=COL2CLASS,
nrows=1L,
check.names=FALSE),
silent=TRUE)
if (!inherits(line1, "try-error"))
return(COL2CLASS)
stop("unable to guess the column names in \"gap\" file '", file, "', sorry")
}
.read.agpORgapFile <- function(agp_or_gap, file)
{
if (agp_or_gap == "agp") {
COL2CLASS <- c(
`chrom`="character",
`chr_start`="integer",
`chr_stop`="integer",
`part_no`="integer",
`part_type`="character",
`gap_len`="character",
`gap_type`="character",
`linkage`="character",
`empty`="character"
)
} else if (agp_or_gap == "gap") {
COL2CLASS <- .guessGapFileCOL2CLASS(file)
} else {
stop("read.Mask internal error: please report")
}
COLS <- c(
"chrom",
"chr_start",
"chr_stop",
"part_type",
"gap_len",
"gap_type"
)
COL2CLASS[!(names(COL2CLASS) %in% COLS)] <- "NULL"
data <- read.table(file,
sep="\t",
col.names=names(COL2CLASS),
colClasses=COL2CLASS,
check.names=FALSE,
fill=TRUE)
}
.read.agpORgapMask <- function(agp_or_gap, file, seqname, mask.width,
gap.types, use.gap.types)
{
if (!isSingleString(seqname))
stop("'seqname' must be a single string")
if (!isSingleNumberOrNA(mask.width))
stop("'mask.width' must be a single integer or 'NA'")
if (!is.integer(mask.width))
mask.width <- as.integer(mask.width)
if (!is.null(gap.types) && (!is.character(gap.types)
|| S4Vectors:::anyMissing(gap.types)
|| anyDuplicated(gap.types)))
stop("'gap.types' must be 'NULL' or a character vector ",
"with no NAs and no duplicated")
if (!isTRUEorFALSE(use.gap.types))
stop("'use.gap.types' must be TRUE or FALSE")
data <- .read.agpORgapFile(agp_or_gap, file)
if (seqname == "?")
.showDistinctSeqnamesAndStop(data$chrom)
data <- data[data$chrom == seqname, ]
ii <- data$part_type == "N"
if (agp_or_gap == "agp") {
data <- data[ii, ]
} else if (!all(ii)) {
warning("gap file contains gaps with a part_type that is not N")
}
if (length(gap.types) == 1 && gap.types == "?") {
found_types <- paste("\"", unique(data$gap_type), "\"", sep="")
found_types <- paste(found_types, collapse=", ")
stop("gap types found in this file for sequence \"", seqname, "\": ", found_types)
}
mask.name <- "AGAPS"
mask.desc <- "assembly gaps"
if (!is.null(gap.types)) {
data <- data[data$gap_type %in% gap.types, ]
mask.desc <- paste(mask.desc, " [type=", paste(gap.types, collapse="|"), "]", sep="")
}
if (nrow(data) == 0)
return(.newEmptyMask(seqname, mask.width, mask.name, mask.desc, mask.desc))
if (agp_or_gap == "agp")
ranges_start <- data$chr_start
else
ranges_start <- data$chr_start + 1L
ranges <- IRanges(start=ranges_start, width=as.integer(data$gap_len))
## Sanity check
if (!identical(end(ranges), data$chr_stop))
stop("broken \"", agp_or_gap, "\" file: contains inconsistent ",
"chr_start/chr_stop/gap_len values ",
"for assembly gaps in sequence \"", seqname, "\"")
if (use.gap.types) {
names(ranges) <- data$gap_type
if (S4Vectors:::isNotStrictlySorted(start(ranges)))
ranges <- ranges[base::order(start(ranges))]
if (!isNormal(ranges))
stop("cannot use the gap types when some gaps are adjacent or overlap")
nir1 <- asNormalIRanges(ranges, force=FALSE)
} else {
nir1 <- asNormalIRanges(ranges, force=TRUE)
}
## Don't use new2(): the validity of the new mask needs to be checked!
new2("MaskCollection", nir_list=list(nir1), width=mask.width, active=TRUE,
NAMES=mask.name, desc=mask.desc, check=FALSE)
}
read.agpMask <- function(file, seqname="?", mask.width=NA, gap.types=NULL, use.gap.types=FALSE)
.read.agpORgapMask("agp", file, seqname, mask.width, gap.types, use.gap.types)
read.gapMask <- function(file, seqname="?", mask.width=NA, gap.types=NULL, use.gap.types=FALSE)
.read.agpORgapMask("gap", file, seqname, mask.width, gap.types, use.gap.types)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### read.liftMask() extracts the AGAPS mask from a UCSC "lift" file.
###
.read.liftFile <- function(file)
{
COL2CLASS <- c(
`offset`="integer",
`xxxx`="NULL", # not sure how to call this
`width`="integer",
`seqname`="character",
`seqlen`="integer"
)
read.table(file,
col.names=names(COL2CLASS),
colClasses=COL2CLASS,
check.names=FALSE)
}
read.liftMask <- function(file, seqname="?", mask.width=NA)
{
if (!isSingleString(seqname))
stop("'seqname' must be a single string")
if (!isSingleNumberOrNA(mask.width))
stop("'mask.width' must be a single integer or 'NA'")
if (!is.integer(mask.width))
mask.width <- as.integer(mask.width)
data <- .read.liftFile(file)
if (seqname == "?")
.showDistinctSeqnamesAndStop(data$seqname)
data <- data[data$seqname == seqname, ]
if (nrow(data) == 0)
return(.newEmptyMask(seqname, mask.width, "AGAPS", "assembly gaps"))
## Sanity checks
seqlen0 <- unique(data$seqlen)
if (length(seqlen0) != 1)
stop("broken \"lift\" file: contains different lengths ",
"for sequence \"", seqname, "\"")
if (!is.na(mask.width) && mask.width != seqlen0)
stop("when supplied, 'mask.width' must match the length found ",
"in the file for sequence \"", seqname, "\"")
contigs0 <- IRanges(start=data$offset+1, width=data$width)
contigs1 <- asNormalIRanges(contigs0, force=TRUE)
if (length(contigs1) != length(contigs0))
warning("some contigs are adjacent or overlapping")
contigs <- Mask(seqlen0, start=start(contigs1), width=width(contigs1))
ans <- gaps(contigs)
names(ans) <- "AGAPS"
desc(ans) <- "assembly gaps"
ans
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### read.rmMask() extracts the RM mask from a RepeatMasker .out file.
###
### See http://www.repeatmasker.org/webrepeatmaskerhelp.html for a
### description of the RepeatMasker output format.
###
.read.rmFile <- function(file)
{
COL2CLASS <- c(
`SW_score`="integer",
`perc_div`="numeric",
`perc_del`="numeric",
`perc_ins`="numeric",
`query_sequence`="character",
`begin_in_query`="integer",
`end_in_query`="integer",
`left_in_query`="character",
`C`="character",
`matching_repeat`="character",
`repeat_class_or_family`="character",
`begin_in_repeat`="integer",
`end_in_repeat`="integer",
`left_in_repeat`="character",
`ID`="character"
)
COLS <- c("query_sequence", "begin_in_query", "end_in_query", "ID")
COL2CLASS[!(names(COL2CLASS) %in% COLS)] <- "NULL"
read.table(file,
col.names=names(COL2CLASS),
colClasses=COL2CLASS,
skip=3,
check.names=FALSE)
}
read.rmMask <- function(file, seqname="?", mask.width=NA, use.IDs=FALSE)
{
if (!isSingleString(seqname))
stop("'seqname' must be a single string")
if (!isSingleNumberOrNA(mask.width))
stop("'mask.width' must be a single integer or 'NA'")
if (!is.integer(mask.width))
mask.width <- as.integer(mask.width)
if (!isTRUEorFALSE(use.IDs))
stop("'use.IDs' must be TRUE or FALSE")
data <- .read.rmFile(file)
if (seqname == "?")
.showDistinctSeqnamesAndStop(data$query_sequence)
data <- data[data$query_sequence == seqname, ]
if (nrow(data) == 0)
return(.newEmptyMask(seqname, mask.width, "RM", "RepeatMasker"))
ranges <- IRanges(start=data$begin_in_query, end=data$end_in_query)
if (use.IDs) {
names(ranges) <- data$ID
if (S4Vectors:::isNotStrictlySorted(start(ranges)))
ranges <- ranges[base::order(start(ranges))]
if (!isNormal(ranges))
stop("cannot use the repeat IDs when some repeats are adjacent or overlap")
nir1 <- asNormalIRanges(ranges, force=FALSE)
} else {
nir1 <- asNormalIRanges(ranges, force=TRUE)
}
## Don't use new2(): the validity of the new mask needs to be checked!
new2("MaskCollection", nir_list=list(nir1), width=mask.width, active=TRUE,
NAMES="RM", desc="RepeatMasker", check=FALSE)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### read.trfMask() extracts the TRF mask from a Tandem Repeats Finder .bed
### file.
###
.read.trfFile <- function(file)
{
COL2CLASS <- c(
`chrom`="character",
`chromStart`="integer",
`chromEnd`="integer",
`name`="character",
`period`="integer",
`copyNum`="numeric",
`consensusSize`="integer",
`perMatch`="integer",
`perIndel`="integer",
`score`="integer",
`A`="integer",
`C`="integer",
`G`="integer",
`T`="integer",
`entropy`="numeric",
`sequence`="character"
)
COLS <- c("chrom", "chromStart", "chromEnd")
COL2CLASS[!(names(COL2CLASS) %in% COLS)] <- "NULL"
read.table(file,
col.names=names(COL2CLASS),
colClasses=COL2CLASS,
check.names=FALSE)
}
read.trfMask <- function(file, seqname="?", mask.width=NA)
{
if (!isSingleString(seqname))
stop("'seqname' must be a single string")
if (!isSingleNumberOrNA(mask.width))
stop("'mask.width' must be a single integer or 'NA'")
if (!is.integer(mask.width))
mask.width <- as.integer(mask.width)
data <- .read.trfFile(file)
if (seqname == "?")
.showDistinctSeqnamesAndStop(data$chrom)
data <- data[data$chrom == seqname, ]
if (nrow(data) == 0)
return(.newEmptyMask(seqname, mask.width, "TRF", "Tandem Repeats Finder"))
ranges <- IRanges(start=data$chromStart+1, end=data$chromEnd)
nir1 <- asNormalIRanges(ranges, force=TRUE)
## Don't use new2(): the validity of the new mask needs to be checked!
new2("MaskCollection", nir_list=list(nir1), width=mask.width, active=TRUE,
NAMES="TRF", desc="Tandem Repeats Finder", check=FALSE)
}
|