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STADEN Unwated format conversion

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Mon Feb 25 05:22:17 EST 2002

In <3C761CC7.43215A48 at bbsrc.ac.uk> Simon Andrews <simon.andrews at bbsrc.ac.uk> writes:
> However, now I think about it, a better solution might be to have an
> option in the Format conversion module which would delete the original
> chromatogram file upon successful conversion to SCF/ZTR format.  This
> would both reduce clutter, and save on disk space, and would mean that
> we end up with a friendly file format.  If you are converting files, I
> can't see many occasions under which you need to keep the originals as
> well (as long as the conversion was successful).

It would make sense if everything held in the ABI file made its way into the
ZTR file, but it does not. The ABI file contains both raw and processed copies 
of the trace, along with temperature, voltage (etc) readouts, various textual
information strings, and lots of other small snippets. My recommended
procedure would be to backup the ABI files and then delete them. Due to the
system specific nature of data backup this isn't really something suited to
automating in pregap4.

In theory ZTR could be updated to support all the ABI records as it's an
extensible format. This would allow true compression of entire ABI files. Our
estimations are that abi-ztr files would be nearly half the size of abi.gz
files. (However such a thing doesn't yet exist.)

One strategy you may wish to consider is that of separating out your input
and output directories. So you have ABI files appearing in ~/incoming/<date>
(for example). After processing the output files go to ~/myproject/. Then the
incoming directory can be completely backed up and removed without needing to
disentangle the files.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Fax: (+44) 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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