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Specifying Files to Process

Pregap4 needs to be given a list of files to process. These files can be binary trace files (in ABI, ALF or SCF format), Experiment Files, or plain text. The files to process do not need to all be in the same format. So if Pregap4 is given a set of mixed ABI and SCF files then the "ABI to SCF conversion" step will only try to convert the ABI files.

It is possible to specify the files to process on the command line at the time of starting up Pregap4. If we have a file named `files' containing three filenames: `xb54a3.s1SCF', `xb54b12.r1LSCF' and `xb54b12.r1SCF', then the first two command lines below are equivalent.

pregap4 -fofn files
pregap4 xb54a3.s1SCF xb54b12.r1LSCF xb54b12.r1SCF
pregap4 *SCF

If the only files ending in `SCF' in this directory were the three listed above then the last command above would also be equivalent to the other two.

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The "Files to Process" dialogue can be brought up from the File menu, or just by pressing the appropriate tab when in compact_win mode.

On the left hand side we have the current list of files to process. This list can be edited simply by clicking with the mouse and typing as normal. This only edits Pregap4's temporary copy of this list and does not modify the contents of any file of filenames that the list was obtained from.

On the right side of the panel we have the Pregap4 output filename prefix and three buttons. The prefix is used when Pregap4 needs to create files for its own use, both for temporary and not so temporary files. For example after processing there may be prefix.passed, prefix.failed files. The prefix defaults to `pregap' until a file of filenames is loaded, in which case it switches to the last used file of filenames.

The three buttons allow loading a new file of filenames, clearing the currently loaded list, and saving the list to a new file of filenames. Note that the "Add file of filenames" button appends to the currently loaded list. To replace it press the clear button first.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_3.html