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

Age	Commit message (Collapse)	Author
2014-03-24	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

2014-01-29	fix warning	Calvin Morrison

2014-01-29	fix corner case	Calvin Morrison

2014-01-29	add filtering based on consecutive mer lengths	Calvin Morrison

2014-01-28	add max_consecutive_binding.py	Calvin Morrison

2014-01-23	update min mer, add fg and bg to parameters	Calvin Morrison

2014-01-22	output parameters	Calvin Morrison

2014-01-22	add different outputs for each run	Calvin Morrison

2014-01-22	rename in script	Calvin Morrison

2014-01-22	split	Calvin Morrison

2014-01-22	fix exit code	Calvin Morrison

2014-01-21	split out score and selection	Calvin Morrison