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Processing Batches Of Mutation Data Trace Files

Cook, Malcolm MEC at Stowers-Institute.org
Mon Apr 7 04:19:50 EST 2003

Dear Staden community,

I am trying to improve on what I understand to be a limitation in using
Staden's pregap4 for mutation detection, at least as it appears to be
advertised in Staden's documentation, and could use your consideration.

The limitation is expressed on page 213 of
http://www.mrc-lmb.cam.ac.uk/pubseq/ftp/docs/manual_unix.pdf as:

"For any batch of readings the reference traces are defined within pregap4's
"Reference Traces" module. Note that this mode of operation, by allowing the
specifcation of only one forward and one reverse trace, limits each batch of
traces processed to those which correspond to a given pair of reference

It is reaffirmed in http://www.mrc-lmb.cam.ac.uk/pubseq/mutations as:

"We recommend that batches of data from single primer pair combinations are
processed separately, using separate temporary gap4 databases"

However, if I'm understanding Staden's architecture correctly, it should be
possible to mix and process traces corresponding drawn from any number of
reference traces.  The approach needs to be one of defining a WT_com proc in
the the [global variables] section of the pregap.config file. The WT_com
proc would access global $lines(ID) and 'figure out' based on some
convention what file should be used as the reference trace.  In my case, my
naming convention embeds the identity of an experimental subject, and I know
that one of my subjects is my 'wild type', and so should be taken as my
reference trace, so I simply need to replace the embedded subject_id with
the subject_id of this wild type.

I'm pretty sure this SHOULD work, but, not being a TCL programmer, I'm
having a little trouble debugging my first and erroneous efforts at writing
the simple string processing routine that implements the above.

If anyone if following me this far, I'd appreciate your comments, and, if
you're interested in helping me with this snippet of tcl, I'd be delighted
to hear from you.

Thanks for you thoughts and time,

Malcolm Cook
Database Applications Manager
Stowers Institute for Medical Research
1000 E 50th Street
Kansas City, MO 64110
tel: 816-926-4449
fax: (816) 926-2098


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