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path: root/src/score_mers.py
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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
2014-03-25Score mer statistics. This closes #6Calvin 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
2014-03-25formatting 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.
2014-03-24Major Updates:Calvin Morrison
SelectiveGenomeAmplication: remove need (again) for any temporary fasta file, instead do all parsing in house with strstreamone and python correctly get reverse compliment. a combination of tac and rev, not just tac add non_melitng and filtered_binding variables to bash for clarity and to reduce clutter score_mers: This should speed up our loading and memory and probably each job since there's less memory overhead. revamp mer points - remove class, save as arrays instead - only allocate mers we need, - don't bother getting counts - reduce command line arguments - use original fasta files now, so it's easier for a user to use (as per issue #5 - remove weird pop_fg/bg functions - add one to total incase of zero div.
2014-03-21add end of sequences in as points in our arrayCalvin Morrison
2014-03-19add output also to scores fileCalvin Morrison
2014-03-18update scoring equationCalvin Morrison
2014-03-13whistpace and 1Calvin Morrison
2014-03-13Refactoring, features, rage!Calvin Morrison
- rename apply filters to filter_mers - return True instead of False - Use this function in score mers - Add total scored check - use np.diff() instead of manually doing it for fg. - fix long line comments - check if len bg_pts <= 1
2014-03-13add coutning points for reversesCalvin Morrison
2014-03-13add comments, add workflow explaination, move pop_{fg,bg} fnsCalvin Morrison
2014-03-13refactor binding layout, add commentsCalvin Morrison
2014-03-05should work:Calvin Morrison
2014-03-05more verbose score outputCalvin Morrison
2014-03-03update defaults and align variable names with global env variablesCalvin Morrison
2014-03-03add load_heterodimer_dic functionCalvin Morrison
2014-03-03check heterodimer dic first because it's likely to be the #1 cause of issuesCalvin Morrison
2014-03-03add check to see if results are even possible, and use gzip outCalvin Morrison
2014-03-03update arguemnts, make {fg,bg}_genome_length globalCalvin Morrison
2014-03-03update parameters fileCalvin Morrison
2014-02-05use a ifilter outsideCalvin Morrison
2014-02-04seperate out scoring stuff into our iterator as a filterCalvin Morrison
2014-02-04add check functions to filter without calling the jobsCalvin Morrison
2014-02-04max_consecutive speed upCalvin Morrison
2014-01-30update score mers with hererodimersCalvin Morrison
2014-01-29add filtering based on consecutive mer lengthsCalvin Morrison