Pregap4 can also be used in a non-interactive environment (in "batch mode"). For this to work it is necessary for pregap4 to already have a valid configuration file with sufficient information for pregap4 to successfully complete the required processing steps. The best way generate this is to take a small set of sequences that you wish to work on and to run Pregap4 interactively on these. Once pregap4 can run and complete and you know that the configuration for that set is correct, use "Save all parameters (in all modules)" from the Modules menu to save the current configuration to disk.
It will then be possible to run pregap4 with the -nowin argument on the
full set of sequences and on any other set that require the same processing
steps. It will be necessary to specify the files to process on the command
line. Then pregap4 will execute the processing steps sending output normally
seen in the output window to the standard output (stdout).
It is possible to have different configuration files for different data sets.
These can be specified on the command line using -config.
pregap4 -nowin -config clip_only.conf -fofn files > files.output
The above example runs pregap4 in batch mode on the files listed in `files'. It will use the previously defined configuration contained in `clip_only.conf' and will save text output to `files.output'. After this processing, the files `files.passed', `files.failed', `files.log' and `files.report' will also have been produced.
If you wish to manually or automatically (via your own script) generate the Pregap4 configuration file instead of using the GUI, please see section Low Level Pregap4 Configuration.