09/11/2006, NTM


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BACKGROUND
##########

NTM_mappingGlobal was generated along with the robot command 
files, by std2robot.pl.
It contains, for each WAMP batch:
- the mappings of batch+variable to ORF name;
- the positions (WAMP plate + well number) of each batch+poolnumber;
- the design file used to generate each batch.

These 3 informations are necessary and sufficient to interpret 
screening results against WAMP pools.

Note concerning the design files: these are micro-pools, so the parts 
have just one 169-bloc per part. At the time we built the command
files, makePartialSTD.pl was not able to make partial design files 
with multiple blocs per part.
Therefore the subdir holding the design files is named 
STD.n2028.q13.k13.parts/ in NTM_mappingGlobal, but this subdir is
now renamed to STD.n2028.q13.k13.blocsPerPart1/.

Example with WAMP batch 2:
- variable 49 represents ORF 11003@31;
- pool number 4 is on WAMP plate 02A, at position 80==H10;
- the design file is STD.n2028.q13.k13.blocsPerPart1/STD.n2028.q13.k13.part1.


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RESULTS
#######

This is all fine, but in fact we screen against the WASP pools,
not the WAMPS. Therefore we need the same 3 informations for
the WASP2 (in 1536 format) and the WASP6 (in 384) pools.
In fact, the necessary knowledge is present in Superposing_9.xls,
along with NTM_mappingGlobal. 

makeBatchMappings.WASPx.pl integrates info from both of these 
files to generate:
- var2orf.WASPx, which holds the mappings between WASP batch+variable
  and ORF;
- coords2pools.WASP<6|2x4>, which says which batch+poolnumber is present
  on each WASP plate + coordinate.

makeC2P.WASP2x16.pl reads coords2pools.WASP2x4, and produces
coords2pools.WASP2x16 for the 1536 plates.


As for the design files corresponding to each WASP batch, they
are known as a consequence of the choices implemented in the
scripts. (Specifically: we decide, arbitrarily, how the WASP
batches are numbered; and this tells us which design corresponds
to each batch number.)

For WASP6, these are regular partial design files, with
blocsPP==6 for batches 1-12 and blocsPP==3 for batch 13.

For WASP2, it's a lot more complex, because when superposing we
have left some plates unchanged (ie just copied the WAMP plates), 
but we did this irrespective of the underlying WAMP batches...
Therefore we produced some batches that correspond to intermediate 
designs, between WAMP and WASP2. For these batches, I have to
generate custom design files, and we must remember to use
a different doDecoding binary, compiled without USING_STD (and
possibly with special code in design.c for maxInterBetweenVars
and maxPoolsPerVar, protected eg with USING_WASP).

I've written makeSplitDesigns.pl to generate the design files 
for these special batches. Once generated, I moved the files
to ../Designs/.

makeBatch2Design.pl builds batch2design.WASPx, which hold
the name of the design file (in ../Designs/) to use for
decoding each WASP batch. These 2 files were also moved
to ../Designs/ after being built.

