The QTL Cartographer system reads and creates many files and each has a default name. For example, the default output file for Rmap is qtlcart.map. We find it convenient to specify a filename stem and allow for the filename extension to indicate which program created it, and what it contains. Suppose we were working on a corn data set. We might use ``corn'' as the filename stem. Then Rmap would write its output to corn.map and its error messages to corn.log. Rqtl would write its output to corn.qtl, etc. Table 1.5 summarizes the standard file name extensions in the QTL Cartographer system. Beginning with version 1.12, the default behavior of QTL Cartographer is to use a filename stem: If none is given, then ``qtlcart'' will be the stem. Unless specifically written in the qtlcart.rc file, the old default names of Rmap.out, Rqtl.out, etc., will no longer be used. These old default names will be used as filetype identifiers. In the output files, there will be a token ``-filetype'' followed by a token from the fourth column of Tables 1.5-1.6. Note that Zmapqtl creates some interim files, and that Preplot will create many other files in addition to the Gnuplot control file: See Section 4.2 for details. The ``-filetype'' specifier will greatly aid programs such as Rmap and Rcross in translating files. As QTL Cartographer develops, this feature will be used more extensively. Once the stem is set in the menu, it will be remembered as long as a resource file is present.
In the interactive menu, if you pick an item to change (say a filename), you can wipe it out by inputting a solitary period. This way, if you had specified an input file in an earlier run, you can delete it.
|
In addition to the files specified in the table, we assume that files with extensions ``maps'' and ``raw'' are Mapmaker/EXP genetic linkage map and raw data files, respectively. These and other files recognized by QTL Cartographer are listed in Table 1.6.