SelectiveWholeGenomeAmplification.git - Parameterized sweeps of FASTA files to help locate useful primers. Work done for Penn bio research guys

Age	Commit message (Collapse)	Author
2014-03-25	add average binding filter	Calvin Morrison

2014-03-25	don't populate, use the bg conts from selectivity	Calvin Morrison

2014-03-25	update header	Calvin Morrison

2014-03-25	fix len	Calvin Morrison

2014-03-25	working upscore_wrapper.sh	Calvin 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
2014-03-25	formatting changes, pylint up in this b****	Calvin Morrison

2014-03-25	remove stray ;	Calvin Morrison

2014-03-25	add score wrapper and SelectiveGenomeUI to make install	Calvin Morrison

2014-03-25	start to add debug variable to score_mers	Calvin Morrison

2014-03-25	Update 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.
2014-03-24	add non-functioning score wrapper	Calvin Morrison

2014-03-24	Major 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.
2014-03-24	use biopython's temperature calculator... slow as dirt	Calvin Morrison

2014-03-24	fix strstream to work with mers list	Calvin Morrison

2014-03-24	add below and fix tabs	Calvin Morrison

2014-03-23	add mer list reading to strstream	Calvin Morrison

2014-03-21	add end of sequences in as points in our array	Calvin Morrison

2014-03-21	fix warning	Calvin Morrison

2014-03-21	add sequence length command	Calvin Morrison

2014-03-19	add output also to scores file	Calvin Morrison

2014-03-18	update scoring equation	Calvin Morrison

2014-03-17	fix issue with readme	Calvin Morrison

2014-03-13	whistpace and 1	Calvin Morrison

2014-03-13	Refactoring, 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
2014-03-13	add coutning points for reverses	Calvin Morrison

2014-03-13	add comments, add workflow explaination, move pop_{fg,bg} fns	Calvin Morrison

2014-03-13	refactor binding layout, add comments	Calvin Morrison

2014-03-13	add message and don't >>	Calvin Morrison

2014-03-06	use kmer_continuous_count instead of kmer_total_count, remove tmp file, ↵	Calvin Morrison
	update parameters for select_mers.py
2014-03-05	fix background as foreground	Calvin Morrison

2014-03-05	should work:	Calvin Morrison

2014-03-05	more verbose score output	Calvin Morrison

2014-03-05	fix type	Calvin Morrison

2014-03-03	update defaults and align variable names with global env variables	Calvin Morrison

2014-03-03	update readnme	Calvin Morrison

2014-03-03	update readnme	Calvin Morrison

2014-03-03	add load_heterodimer_dic function	Calvin Morrison

2014-03-03	check heterodimer dic first because it's likely to be the #1 cause of issues	Calvin Morrison

2014-03-03	add check to see if results are even possible, and use gzip out	Calvin Morrison

2014-03-03	update arguemnts, make {fg,bg}_genome_length global	Calvin Morrison

2014-03-03	update parameters file	Calvin Morrison

2014-02-17	output filters into output directory not temp to enable multiple runs at once	Calvin Morrison

2014-02-05	use a ifilter outside	Calvin Morrison

2014-02-04	seperate out scoring stuff into our iterator as a filter	Calvin Morrison

2014-02-04	add check functions to filter without calling the jobs	Calvin Morrison

2014-02-04	max_consecutive speed up	Calvin Morrison

2014-02-04	update save locations	Calvin Morrison

2014-01-30	update score mers with hererodimers	Calvin Morrison

2014-01-29	fix warning	Calvin Morrison

2014-01-29	rm	Calvin Morrison