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ABI File Formats

James Bonfield jkb at mrc-lmb.cam.ac.uk
Fri Jun 13 03:33:47 EST 1997

David Campbell wrote:

>We are using the Staden package (primarily pregap) to "clean-up" sequences
>prior to placing them in a blast searchable database.  All of the data is
>collected on ABI sequencers, however some of the files seem to be improperly
>parsed by pregap, and these same files are not visible using the version of
>ted that we are using.

Is it possible that you could email us any of these problematic ABI files? I
find it odd that 373 ones don't work where 377 ones do as the code was written
to read 373 files and it's simply luck that it doesn't appear to have changed
appreciably in the 377 output.

Also, try using trev instead of ted. (Trev is more up to date.)

>We suspect there is a difference in the file formats
>between the two, but the person I talked to at ABI said that their file
>formats were proprietary. 

Sounds familier. For what it's worth, we haven't seen much difference in any
of the file formats. The one thing that I have seen to cause us problems is
with ABI files that have been hand edited (using the ABI software) on the Mac.
The edits seem to be stored in a slightly different fashion which breaks our
software. Unfortunately we too have never had access to the official file

>(PS we are collecting data on a Macintosh, then transferring the data in
>MacBinary mode to a sparc station)

It's worth trying again with Binary transfer. MacBinary adds on ther macintosh
resource fork to the start of the files, which the unix tools then have to try
and strip off (not always reliably).

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 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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