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#PrimerTree
#Copyright (C) 2013 Jim Hester
#' Query a pair of primers using ncbi's Primer-BLAST, if primers contain iupac
#'
#' ambiguity codes, enumerate all possible combinations and combine the
#' results.
#' @param forward forward primer to search by 5'-3' on plus strand
#' @param reverse reverse primer to search by 5'-3' on minus strand
#' @param num_aligns number of alignment results to keep
#' @param num_permutations the number of primer permutations to search, if the degenerate bases
#' cause more than this number of permutations to exist, this number will be
#' sampled from all possible permutations.
#' @param ... additional arguments passed to Primer-Blast
#' @param .parallel if 'TRUE', perform in parallel, using parallel backend
#' provided by foreach
#' @param .progress name of the progress bar to use, see 'create_progress_bar'
#' @return httr response object of the query, pass to \code{\link{parse_primer_hits}} to parse the results.
#' @export
primer_search = function(forward, reverse, num_aligns=500, num_permutations=25, ..., .parallel=FALSE, .progress='none'){
if(missing(forward) || missing(reverse))
BLAST_primer()
primers = enumerate_primers(forward, reverse)
num_primers = nrow(primers)
if(num_primers > num_permutations){
warning(immediate.=T, 'primers have ', num_primers, ' possible combinations due to degenerate bases, sampling ', num_permutations, " primers, use 'num_permutations' to change")
primers = primers[ sample.int(num_primers, num_permutations, replace=F), ]
}
message('BLASTing ', nrow(primers), ' primer combinations')
#enumerate all combinations to handle ambiguity codes
alply(primers, .margins=1, .expand=F, .parallel=.parallel, .progress=.progress,
function(row) BLAST_primer(row$forward, row$reverse, num_targets_with_primers=max(num_aligns %/% nrow(primers), 1), ...))
}
iupac = list( "M" = list("A", "C"),
"R" = list("A", "G"),
"W" = list("A", "T"),
"S" = list("C", "G"),
"Y" = list("C", "T"),
"K" = list("G", "T"),
"V" = list("A", "C", "G"),
"H" = list("A", "C", "T"),
"D" = list("A", "G", "T"),
"B" = list("C", "G", "T"),
"N" = list("A", "C", "G", "T"),
"I" = list("A", "T", "C"))
enumerate_primers = function(forward, reverse){
forward_primers = enumerate_ambiguity(forward)
data.frame(forward=forward_primers,
reverse=rep(enumerate_ambiguity(reverse),
each=length(forward_primers)),
stringsAsFactors = FALSE)
}
enumerate_ambiguity = function(sequence){
search_regex = paste(names(iupac), collapse='|')
locs = str_locate_all(sequence, search_regex)
sequences = list()
count = 1
for (i in seq_len(nrow(locs[[1]]))){
loc = locs[[1]][i,]
ambiguity = str_sub(sequence, loc[1], loc[2])
for(type in iupac[[ambiguity]]){
new_seq = sequence
str_sub(new_seq, loc[1], loc[2]) <- type
sequences[[count]] = enumerate_ambiguity(new_seq)
count = count + 1
}
return(unlist(sequences))
}
return(sequence)
}
print_options = function(options){
output = capture.output( print(
options[ is.na(options$type) | options$type != 'hidden',
c('name', 'type', 'defval') ])
)
message(paste(output, "\n", sep=""))
}
BLAST_primer = function(forward, reverse, ..., organism='',
primer_specificity_database='nt', exclude_env='on'){
url = 'https://www.ncbi.nlm.nih.gov/tools/primer-blast/'
form = GET_retry(url)
content = parsable_html(form)
all_options = get_options(content)
if(missing(forward) || missing(reverse)){
print_options(all_options)
stop('No primers specified')
}
options = list(..., primer_left_input=forward, primer_right_input=reverse,
organism=organism,
primer_specificity_database=primer_specificity_database,
exclude_env=exclude_env,
search_specific_primer='on')
names(options) = toupper(names(options))
match_args = pmatch(names(options), all_options$name)
bad_args = is.na(match_args)
if(any(bad_args)){
print_options(all_options)
stop(paste(names(options)[bad_args], collapse=','), ' not valid option\n')
}
options = get_defaults(options, all_options)
start_time = now()
message('Submitting Primer-BLAST query')
response = POST_retry(paste(url, 'primertool.cgi', sep=''), body=options)
values = get_refresh_from_meta(response)
while(length(values) > 0){
message('BLAST alignment processing, refreshing in ', values[1], ' seconds...')
Sys.sleep(values[1])
response = GET_retry(values[2])
values = get_refresh_from_meta(response)
}
total_time = start_time %--% now()
message('BLAST alignment completed in ', total_time %/% seconds(1), ' seconds')
response
}
#modify a function to check the status and retry until success
retry = function(fun, num_retry=5, ...){
function(...){
res = fun(...)
itr = 0
status = http_status(res)
while(itr < num_retry && inherits(res, 'response') && tolower(status$category) != 'success'){
warning('request failed, retry attempt ', itr+1)
res = fun(...)
status = http_status(res)
itr = itr + 1
#sleep to avoid hitting NCBI query rate limit :'-(
Sys.sleep(0.4)
}
res
}
}
GET_retry = retry(GET)
POST_retry = retry(POST)
#' Parse the primer hits
#'
#' @param response a httr response object obtained from \code{\link{primer_search}}
#' @export
parse_primer_hits = function(response){
content = parsable_html(response)
rbind.fill(xpathApply(content, '//pre', parse_pre))
}
parse_a = function(a){
#links like entrez/viewer.fcgi?db=nucleotide&id=452085006
m = regexpr('id=\\d+', xmlAttrs(a)['href'])
gi = gsub('id=', '', unlist(regmatches(xmlAttrs(a)['href'], m)))
if(length(gi) == 0L){
#links like nucleotide/449036831?from=1107741&to=1107929&report=gbwithparts
m = regexpr('nucleotide/\\d+', xmlAttrs(a)['href'])
gi = gsub('nucleotide/', '', unlist(regmatches(xmlAttrs(a)['href'], m)))
}
if(length(gi) == 0L) gi = NA
data.frame(gi=as.character(gi), accession=as.character(xmlValue(a)))
}
parse_pre = function(pre){
pre_text = xmlValue(pre)
a = getNodeSet(pre, './preceding-sibling::a[1]')
if(length(a) <= 0)
stop('Parsing failed for ', pre_text)
ids = parse_a(a[[1]])
product_length_regex = 'product length = (\\d+)'
template_regex = 'Template[^\\d]+(\\d+)[^.ACGT]+([.ACGT]+)[^\\d]+(\\d+)'
full_regex = paste('[\\S\\W]*', product_length_regex, '[\\S\\W]*?',
template_regex, '[\\S\\W]*', template_regex, '[\\S\\W]*', sep='')
values = str_split(gsub(full_regex, paste('\\', 1:8, sep='', collapse='|'),
pre_text, perl=T), '[|]')[[1]]
data.frame(ids,
product_length=as.numeric(values[1]),
mismatch_forward=str_count(values[3], '[ACGT]'),
mismatch_reverse=str_count(values[6], '[ACGT]'),
forward_start = as.numeric(values[2]),
forward_stop = as.numeric(values[4]),
reverse_start = as.numeric(values[5]),
reverse_stop = as.numeric(values[7]),
product_start=min(as.numeric(values[c(2,4,5,7)])),
product_stop=max(as.numeric(values[c(2,4,5,7)]))
)
}
get_refresh_from_meta = function(response){
content = parsable_html(response)
meta = content['//meta[@http-equiv="Refresh"]']
if(length(meta) > 0){
values = str_split(xmlAttrs(meta[[1]])['content'], '; URL=')[[1]]
return(values)
}
return()
}
get_defaults = function(set_options, options){
#only look at values with set defaults
options = options[ !is.na(options$defval), ]
unchanged_options = setdiff(options$name, names(set_options))
default_values = as.character(options[ match(unchanged_options, options$name), 'defval' ])
names(default_values) = unchanged_options
c(set_options, default_values)
}
get_options = function(content){
options = rbind.fill(xpathApply(content, '//form//input | //form//select', parse_attributes))
options$type = as.character(options$type)
#add dropdown type if they are NA
options$type[is.na(options$type)] <- 'dropdown'
#make default values for checkboxes on or off rather than checked or unchecked
options$defval = as.character(options$defval)
check_map = c('checked' = 'on', 'unchecked' = '')
checkboxes = which(options$type == 'checkbox')
options$defval[ checkboxes ] = check_map[ options$defval[ checkboxes ] ]
options[ options$type != 'hidden', c('name', 'type', 'defval') ]
}
parse_attributes = function(x){
as.data.frame(t(xmlAttrs(x)))
}
parsable_html = function(response){
txt <- content(response, as='text', encoding='UTF-8')
# remove any unicode characters
Encoding(txt) <- "UTF-8"
txt <- iconv(txt, "UTF-8", "ASCII", sub = "")
#this gsub regex is to remove the definition lines, some of which have
# bracketed <junk> in them, which messes up the parsing
txt <- gsub('("new_entrez".*?</a>).*?<pre>\n\n', '\\1\n<pre>', txt)
htmlParse(txt)
}
filter_duplicates = function(hits){
location_columns = c('accession', 'forward_start', 'forward_stop', 'reverse_start', 'reverse_stop')
hits[!duplicated(t(apply(hits[location_columns], 1, range))),]
}
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