first previous next last contents

Command Line Arguments

Typically for interactive use of Pregap4 you need to type nothing more than pregap4. For the more inquisitive user the following command line options are available.

-config config_file
This specifies an alternative configuration file to Pregap4. The default configuration file is named `pregap4.config'. It is valid to specify a filename which does not yet exist. This filename will be used for both reading and writing configurations to.

-fofn filename
Specifies a file of filenames for processing. Multiple uses of -fofn are allowed and they are additive. The default prefix for Pregap4 output files is derived from the last specified file of filenames.

-nowin
-no_win
These are synonyms. They prevent Pregap4 from displaying its graphical user interface and force it to automatically "Run". This argument should only be used when driving Pregap4 as a batch job. It is necessary to create a valid configuration file before using -nowin.

-win_compact
This uses a compact GUI mode with the main dialogues listed as separate tabs in the main window. This can be made the default display style by selecting "Compact Window Style" in the Options menus. The command line option overrides this default. See section Window Styles.

-win_separate
This uses a GUI mode using separate top level windows in a similar manner to Gap4, Nip4 and Sip4. This can be made the default display style by selecting "Separate Window Style" in the Options menus. The command line option overrides this default. See section Window Styles.
--
Indicates the end of Pregap4 options. This is used incase filenames start with a minus sign, to distinguish filenames from possible Pregap4 options.

The remaining arguments on the command line are assumed to be filenames. For example the following command executes Pregap4 in batch mode using configuration file `batchX' on all files in the current directory named something.SCF.

pregap4 -config batchX -nowin -- *.SCF

The -- in the above example is to guard against the unlikely case where *.SCF could match a filename starting with minus.


first previous next last contents
This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_2.html