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MakeSCF

NAME

makeSCF -- Converts trace files to SCF files.

SYNOPSIS

makeSCF [-8] [-2] [-3] -(abi|alf|scf|pln) input_name [-compress compression_mode] [-normalise [-output output_name]

DESCRIPTION

MakeSCF converts trace files to the SCF format. It can input ABI 373A, Pharmacia A.L.F., or previously created SCF files (although converting from SCF to SCF serves no valid purpose!). Previous versions of makeSCF also performed the estimation of base accuracy. This is no longer an integral part of makeSCF; use the eba program on the produced SCF file.

OPTIONS

-8
Force conversion to 8 bit sample data. This shrinks the size of SCF files using 16 bit sample values, but at a loss of resolution. For trace display purposes this accuracy loss is acceptable.
-2
Force the output to be written in SCF version 2. By default the latest version (3) is used.
-3
Force the output to be written in SCF version 3. This is the default.
-s
Silent mode. This prevents the output of the copyright message.
-abi, -alf, -scf, -any
Specify an input file format. A file format of any will force makeSCF to automatically determine the correct input file type.
-compress compression_mode
Requests the generated SCF file to be passed through a separate compression program before writing to disk. makeSCF does not contain any compression algorithms itself. It requires the appropriately named tool to be on the system and in the user's PATH. Valid responses for compression_mode are (in order of best compression first) bzip, gzip, compress and pack. Note that bzip at present is only bzip version 1 and that bzip version 2 is incompatible.
-normalise
Performs some very simple trace normalisation. This subtracts the background signal (by defining the background signal to be the lowest of the four traces) and rescales the peak heights, averaging the height over a `window' of 1000 trace sample points. This option may well be useful for some unscaled ALF files.
-output file
Specifies the filename for the SCF file to be produced. If this is not specified the SCF file will be sent to standard output.

EXAMPLES

To convert an ABI 373A trace:

makeSCF -8 -abi trace.abi -output trace.scf

To convert an ALF archive to individual SCF files (Warning! this will most certainly fail if your clone names contain spaces):

alfsplit trace.alf | awk '/^Clone/ {print $3 "ALF"}' > trace.files

sh -c 'for i in `cat trace.files`;do makeSCF -alf $i -output
    $i.scf;done

NOTES

If ABI and A.L.F files are edited before input to makeSCF the contents of the resulting SCF files are unpredictable. To use Pharmacia A.L.F. files the alfsplit program should first be used. Then makeSCF should be run on each of the split files. See the example above.

CONV, CONV, MACH, DATF and DATN comment identifiers and values are written to the SCF file.

SEE ALSO

See section scf(4).
See section eba(1).


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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/manpages_7.html