Easier to use CAD for this! SFTOOLS is too clever.. Eleanor On 7 January 2015 at 03:45, Seth Harris <set...@gmail.com> wrote:
> Hi all, > > I have a heterogeneous collection of mtz files I'm trying to whip into > some kind of standardized vocabulary shape, namely setting column names and > types so that subsequent scripts can sensibly make maps and so forth. I > have set up the ever-useful sftools to do most of this, but of course > sftools scripts rely on one providing a series of answers to questions you > think it is going to ask, and by its own admission it was designed to be > used interactively and includes various "protections" which, also by its > own admission, makes it harder to use it in batch mode... Because it finds > files with interesting columns (e.g. only 1's and 0's) that prompt it to > ask you unexpected questions (e.g. is this an X-plor Rfree column? despite > the "Rfree_flag title and the 5% population of 1's ; ). , for which your > prescribed answers no longer apply (and my log files end up with inane > computer v computer dialogues like "You must answer Y or N! You must answer > Y or N! You must answer...etc.") > > So, presumably the number of exceptional cases is finite (though tedious) > and I can just carry on dealing with them one after the other and learn to > be a better coder, but... > > My question: is there some way to turn off these protections (i.e. please > just read in the file without question!), or some version of SFTOOLS that > is more batch-friendly about which I'm not yet aware? It would be nice to > have something that can more programmatically interrogate mtz column > headers and respond sensibly rather than this kind of 20 questions you do > when you have to read the header and then parse the names and then ask a > series of "is it Rfree?" "is it CV?" "is it bigger than a breadbox?" type > stuff. > > Again, I know the sftools documentation is clear that the design goal was > for interactive use and humans have little trouble with such questions, but > when there might be several thousand of them... > > Thanks for any pointers or alternatives! > > Seth > > >
