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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
2014-03-25add score wrapper and SelectiveGenomeUI to make installCalvin 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
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.
2014-03-24use biopython's temperature calculator... slow as dirtCalvin Morrison
2014-03-24fix strstream to work with mers listCalvin Morrison
2014-03-24add below and fix tabsCalvin Morrison
2014-03-23add mer list reading to strstreamCalvin Morrison
2014-03-21add end of sequences in as points in our arrayCalvin Morrison
2014-03-21fix warningCalvin Morrison
2014-03-21add sequence length commandCalvin Morrison
2014-03-19add output also to scores fileCalvin Morrison
2014-03-18update scoring equationCalvin Morrison
2014-03-17fix issue with readmeCalvin 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
2014-03-13add message and don't >>Calvin Morrison
2014-03-06use kmer_continuous_count instead of kmer_total_count, remove tmp file, ↵Calvin Morrison
update parameters for select_mers.py
2014-03-05fix background as foregroundCalvin Morrison
2014-03-05should work:Calvin Morrison
2014-03-05more verbose score outputCalvin Morrison
2014-03-05fix typeCalvin Morrison
2014-03-03update defaults and align variable names with global env variablesCalvin Morrison
2014-03-03update readnmeCalvin Morrison
2014-03-03update readnmeCalvin 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
2014-02-17output filters into output directory not temp to enable multiple runs at onceCalvin 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
2014-02-04update save locationsCalvin Morrison
2014-01-30update score mers with hererodimersCalvin Morrison
2014-01-29fix warningCalvin Morrison
2014-01-29rmCalvin Morrison