Fragman and seqinr have their own (identical?, different from sangerseqR) read.abif fxns. Trying to use this as a model for the reverse process I don't get anywhere ... any suggestions? Here is some of what i have done:

##### read binary as in Fragman's read.abif function #####

fh <- file("input.ab1", open="rb") fh description class "input.ab1" "file" mode text "rb" "binary" opened can read "opened" "yes" can write "no" rd <- readBin(fh, what="raw", n=1.2 *file.info("pGem-CP1-1768794_H12.ab1")$size), endian="little")

# rd is hexadecimal

##### check what was imported #####

summary(rd) Length Class Mode 291025 raw raw

##### import the data as it would be worked on #####

library(Fragman)

abif <- read.abif("input.ab1") summary(abif) Length Class Mode Header 10 -none- list Directory 7 data.frame list Data 130 -none- list

##### try to write binary with the imported data #####

newfh <- file("new.ab1", "wb") newfh description class mode text opened can read "new.ab1" "file" "wb" "binary" "opened" "no" can write "yes"

writeBin(abif, newfh, endian="little") Error in writeBin(abif, newfh, endian = "little") : can only write vector objects writeBin(as.vector(abif), newfh, endian="little") Error in writeBin(as.vector(abif), newfh, endian = "little") : can only write vector objects writeBin(as.vector(unlist(abif)), newfh, endian="little") close(newfh)

# ab1 file is written but cannot be read as ab1

input.ab1 ~ 291kb newer.ab1 ~ 503kb