In case MapMapping section is used, the map translation table can be generated by command printmapping.

Imagine that the map names in the file for a map set "TAIR10" have no matching maps with the same name in the database. For example, the map name in the file is "1" while the corresponding name in the database is "Chr.1". Instead, the map "Chr.1" has accession number "1". If the MapMapping section is not used, the program would expect that the map names in the file are identical to the map names in the database. But in our case, the translation of names is necessary. As we know that the map names in file correspond to accession number in the database, the first column of the translation table should have AccessionNo and the second column can contain MapId or MapName or even AccessionNo. The main point is to tell the program that the map names in the file are NOT identical to the names in the database. The exact command linking map names in the file to MapId would be:

printmapping "Arabidosis thaliana/TAIR10" AccessionNo MapName

The output for this command set would be:

"1"="Chr.1"
"2"="Chr.2"
"3"="Chr.3"
"4"="Chr.4"
"5"="Chr.5"

This table can be copied to the MapMapping section of the corresponding INI file.

Note

It is quite common to use the command line mode (as opposed to the interactive one), so that the output of the command could be redirected to a file.