counter =
function(max = 10)
{
counts = numeric()
numRecords = 0
read = function(txt) {
id = gsub("^>(.*) .*", "\\1", txt)
vals = table(id)
for(id in names(vals))
counts[id] <<- ifelse(id %in% names(counts), counts[id], 0) + vals[id]
numRecords <<- numRecords + 1
if(numRecords >= max) {
msg = list(message = "Reached maximum count")
class(msg) = c("CountException", "error", "condition")
stop(msg)
}
# sum(nchar(txt))
}
list(read = read, counts = function() counts)
}
theCount = counter()
f = chunk2LineReader(theCount$read)
x = postForm("http://www.wormbase.org/db/searches/advanced/dumper",
species = "elegans",
list = "AC3.8 M7 X IV III:1000..4000",
feature = "BLASTX Hits",
DNA = "feature coordinates only",
flank5 = "0",
flank3 = "0",
relative = "Chromosome",
orientation = "Relative to feature",
dump = "Plain TEXT",
DUMP = "DUMP",
.cgifields = c("feature", "orientation", "dump", "relative", "DNA"),
.opts = list(writefunction = f$read))
nchar(x)
# DNA = 'feature and flanking sequences',
# DUMP = 'DUMP',
#species = 'elegans',
x = postForm('http://www.wormbase.org/db/searches/advanced/dumper',
species="briggsae",
list="AC3.8 M7 X IV III:1000..4000",
flank3="0",
flank5="0",
feature="Gene Models",
dump = "Plain TEXT",
orientation = "Relative to feature",
relative = "Chromsome",
DNA ="flanking sequences only",
.cgifields = paste(c("feature", "orientation", "DNA", "dump", "relative"), collapse=", "))
print(x)
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