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==September 11== *'''TO DO:''' **Modify Perl probe generation script to read files in Cosmic set format (like above) **Post new Perl script here **Run tests, compare new results to old Cosmic set results **Show Dr. Zhang the code *'''Cosmic File Reading''' **Need to modified Perl script so that Cosmic set type files can be read in successfully. **Also need to make sure that Gene and Exon IDs are output by the final program; otherwise it will be very difficult to keep track of probes. **These modifications have been made; an in-file setting now controls what file format to load from. *'''Fixing errors with some probes''' **It was discovered that some probe sets were causing errors while others were not; this was related to the way Perl's "return" function works. The probeList variables were not undefined, as they contained a single number with the error code for not finding any compatible probes. **This was fixed. *'''New Perl Script''' **[[Media:GetProbes 091108.txt|GetProbes 091108.txt]] *'''NEW: Redundant Sequences''' **Now, need to figure out a better way to deal with redundant portions of various genes. **Basically, different genes that include the same exon. **New data structure? ***Perhaps create exonIDs for various genes? Then, list genes as a combination of exons in this database? ***Prevents overlap. **Added refGene data from UCSC to a mysql table called refGene on laptop. ***Data can be ordered by chromosome, txStart and end regions. **However, multiple exons are stored in single rows. **A script could be used (PHP?) to extract each exon and create a new database table. **''Redundant Sequence Script Idea:'' ***Use PHP. ***Scan through table; grab all values from exonStarts and exonEnds (these are our exons.) ***For each exon, also grab the "name" field, the "chr" field, and the "strand" field. ***Reprint out new exons using a basic incrementing ID. Also reprint out gene data in a new table as well. '''Table Exon - Fields:''' exonID (autoincrement) chr strand start end '''Table ExonLink - Fields:''' geneID exonID position NOTE: There will be multiple entries for each geneID. In order to figure out which exons to sequence for a given gene, all exonIDs will be pulled out of the database. Probes for each exonID will be designed. Example: SELECT exonID FROM TABLE gene WHERE geneID=''geneid_value'' *'''After this is finished, probes can be ordered using new code.'''
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