Nothing
funX <- function(megProj, acc.tab, taxa, max.bp, align.exe, logfile){
conn <- dbconnect(megProj@db)
seqs <- dbReadDNA(conn, acc.tab, taxa, max.bp,
enforce.binomial = TRUE)
slog(paste("\n-- ", ifelse(is.list(seqs), length(seqs), nrow(seqs)),
" seqs. of ", taxa, sep = ""), file = logfile)
seqs <- mafft(seqs, method = "auto", path = align.exe)
## Vitis vinifera + trnLF:
## bad sequences make alignment longer than max.bp
if ( ncol(seqs) > max.bp ){
d <- dist.dna(seqs, model = "N", pairwise.deletion = TRUE,
as.matrix = TRUE)
n.zero <- apply(d, 2, function(x) length(x[x == 0]))
n.zero <- which.max(n.zero)
exclude <- rownames(d)[d[, n.zero] > 10]
seqs <- deleteEmptyCells(seqs[!rownames(seqs) %in% exclude, ])
exclude <- lapply(exclude, splitGiTaxon)
exclude <- do.call(rbind, exclude)[, "gi"]
SQL <- paste("UPDATE", acc.tab,
"SET status = 'excluded (too distant)'",
"WHERE", sql.wrap(exclude, term = "gi"))
dbSendQuery(conn, SQL)
slog("\n-- NOTE:", length(exclude), "seqs. of", taxa, "excluded", file = logfile)
}
dbWriteDNA(conn, acc.tab, seqs, enforce.binomial = FALSE,
status = "aligned")
dbDisconnect(conn)
}
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