Nothing
"pfam" <- function(id, alignment='seed', verbose=FALSE) {
##alignment <- 'full' ## seed, ncbi, full, metagenomics
oops <- requireNamespace("RCurl", quietly = TRUE)
if(!oops)
stop("Please install the RCurl package from CRAN")
cl <- match.call()
format <- "fasta"
url = paste('http://pfam.xfam.org/family/', id, '/acc', sep='')
if(verbose)
cat("Fetching accession from", url, "\n")
if(!RCurl::url.exists(url)) {
cat(url, "\n")
stop("Url does not exist")
}
accid <- readLines(url, warn=FALSE)[1]
## download alignment
url <- paste('http://pfam.xfam.org/family/', accid,
'/alignment/', alignment, '/format?format=', format, sep='')
if(verbose)
cat("Fetching alignment from", url, "\n")
if(!RCurl::url.exists(url)) {
cat(url, "\n")
stop("Url does not exist")
}
tmpfile <- tempfile()
success <- download.file(url, tmpfile, quiet=!verbose)
if(success==1)
stop("Download failed")
if(verbose)
cat("Alignment successfully downloaded (", tmpfile, ")\n")
fasta <- read.fasta(tmpfile)
unlink(tmpfile)
fasta$call=cl
return(fasta)
}
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