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2014-06-25really reduce memory usage of select_mers.pyCalvin Morrison
2014-05-20score regardlessCalvin Morrison
2014-05-20fix div by zeroCalvin Morrison
2014-04-23simplify select_mers.pyCalvin Morrison
2014-04-20force bash on lockCalvin Morrison
2014-04-18force 2.7Calvin Morrison
2014-04-14keep asking for files if they don't exist, filter melting temperature with ↵Calvin Morrison
updated function
2014-04-14added new stuff for filter melting temperatureCalvin Morrison
2014-04-14don't use strstream, use kmer_locationsCalvin Morrison
2014-04-14mkdir on lock claimCalvin Morrison
2014-04-08more docs and add strandCalvin Morrison
2014-04-08add lockCalvin Morrison
2014-04-08update arg infoCalvin Morrison
2014-04-07tabular outputCalvin Morrison
2014-04-07working output full genome.pyCalvin Morrison
2014-04-07fix stream counting so it doesn't count overCalvin Morrison
2014-04-07initial commit of output_full_genome.pyCalvin Morrison
2014-04-07add genome lengthCalvin Morrison
2014-04-07+x average_bindingCalvin Morrison
2014-04-07fix reverse counts and output genome lengthCalvin Morrison
2014-04-02add exit codesCalvin Morrison
2014-04-01remove a debug lineCalvin Morrison
2014-04-01add feature to read from previously scored all-scores file, clean up code as ↵Calvin Morrison
well
2014-04-01check exit status and more error checking in check_feasilbeCalvin Morrison
2014-03-31fix bug in using combination file. this closes #18Calvin Morrison
2014-03-31add UI for scorign func, update doc and varaiblesCalvin Morrison
2014-03-31add scorign to header and paramters and suchCalvin Morrison
2014-03-31add custom scoringCalvin Morrison
2014-03-31proper sizes with custom mersCalvin Morrison
2014-03-31This closes bug #19. adds variables into the scoring header for later referenceCalvin Morrison
2014-03-31Add feature to have a top-scores file. closes issue #21Calvin Morrison
2014-03-27Scoring all mer combinations from a file with a -mCalvin Morrison
2014-03-27improve output, add number of primers in first colum. this closes #12Calvin Morrison
2014-03-27move stuff aroundCalvin Morrison
2014-03-27Add scoring for specific combinations.Calvin Morrison
- add scoring for specific combos - update readme - add CLI args for score_mers.py - update score_wrapper - use more generic print functions in score_mers
2014-03-26majorly rewrite and revamp the script to support runnign parts at a timeCalvin Morrison
2014-03-26add primer_weight to our score functionCalvin Morrison
2014-03-26use floatCalvin Morrison
2014-03-25Score mer statistics. This closes #6Calvin Morrison
2014-03-25update selectivity equation, and update readmeCalvin Morrison
2014-03-25add average binding filterCalvin Morrison
2014-03-25don't populate, use the bg conts from selectivityCalvin Morrison
2014-03-25update headerCalvin Morrison
2014-03-25fix lenCalvin Morrison
2014-03-25working upscore_wrapper.shCalvin Morrison
Score wrapper essentially does a few things 1) backgrounds score_mers.py 2) creates an intercept for any Ctrl+C 3) waits for score_mers.py to finish 4) if there's an intercept, send a SEGV to the process and try and exit it works, it might be dirty, you might see some output... but still at least you can exit now
2014-03-25formatting changes, pylint up in this b****Calvin Morrison
2014-03-25remove stray ;Calvin Morrison
2014-03-25start to add debug variable to score_mersCalvin Morrison
2014-03-25Update scoring function.Calvin Morrison
Before we were incorrectly scoring our background. Using the new equation: score = (nb_primers * fg_mean_dist * fg_variance_dist) / (bg_ratio) where bg_ratio is bg_genome_length / count_of_bg_mers This will be faster, and will simplify our code (no whcky appends or anything. It can be even faster if we want to by not even storing the background points, just their hits. Should be relatively easy to do that.
2014-03-24add non-functioning score wrapperCalvin Morrison
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