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==September 12== *'''TO DO:''' **Finish script that creates new tables. *'''Script to create refExon and refExonLink''' **Created a PHP script that can build the two new tables (refExon and refExonLink). **In order to differentiate between coding and non-coding regions, in the refExonLink table, I have added two columns: codeStart and codeEnd. **Basically, these two values allow us to figure out what is coding and what is not in the following way. **Cases: ***Out of bounds xxxxxx | | OR | | xxxxxx Both codeStart and codeEnd will be set to -1. ***In bounds | xxxxxx | Both codeStart and codeEnd will be set to -10. ***Overlap xxxx|xxx | codeStart will be set to the starting point of coding, codeEnd will be set to -10. | xxxx|xxx codeStart will be set to -10, codeEnd will be set to the end point of coding. xx|xxx|xx codeStart will be set to the starting point of coding, codeEnd will be set to the end point of coding. **This should allow coding and non-coding regions to be identified by the probe generation script. **Finished script; ran script on all RefSeq exons! **All refseq exons are now present in a mysql database on laptop. *'''Test with probe generation code''' **Using "SELECT INTO FILE," a set of exons was created to test the probe generation code. **Uploaded file to pgp.oxf, testing it now. ***Due to "brute-force" algorithm for genes, it seems to be taking a long time; make sure script is working. *'''Script test results''' **For now, I have disabled loading the KmerDist, as the code is not using Uniqueness calculations at the moment. This stops an initial delay during testing. **With small exons, script seems to work well; I had to lower the minimum target size to do this however, as some small exons were not working (small boundary arm length). **Large exons have a problem, however. ***Too many possible Oligos; code takes far too long for this to be feasible. **Options: ***Split large exons into two pieces. ***Find better algorithms to deal with large exons. ***Use much more stringent cutoffs for large exons.
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