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

Age	Commit message (Collapse)	Author
2014-04-07	Rename!	Calvin Morrison

2014-04-03	add scoring to paramters	Calvin Morrison

2014-04-02	use min	Calvin Morrison

2014-04-02	add sort_by support for top-scores	Calvin Morrison

2014-03-31	update folder name	Calvin Morrison

2014-03-31	add scorign to header and paramters and such	Calvin Morrison

2014-03-31	This closes bug #19. adds variables into the scoring header for later reference	Calvin Morrison

2014-03-31	fix sort	Calvin Morrison

2014-03-31	Add feature to have a top-scores file. closes issue #21	Calvin Morrison

2014-03-27	Add support for ignoring all mers. and more	Calvin Morrison
	- add a check for filters. quit if no mers make it - add a final fg mer selection file in the $current_run folder - add a filter/ folder as not to clutter the current run - fix double quote syntax - add option for ignore all for the UI
2014-03-27	add ability to ignore all mers from a file	Calvin Morrison

2014-03-26	majorly rewrite and revamp the script to support runnign parts at a time	Calvin Morrison

2014-03-26	add primer_weight to our score function	Calvin Morrison

2014-03-25	update selectivity equation, and update readme	Calvin Morrison

2014-03-25	add average binding filter	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.
2014-03-13	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
2014-03-03	update defaults and align variable names with global env variables	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

2014-02-04	update save locations	Calvin Morrison

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

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

2014-01-21	add output file	Calvin Morrison

2014-01-20	really use global	Calvin Morrison

2014-01-20	use global select_mers.py	Calvin Morrison

2014-01-20	updated script and ui	Calvin Morrison

2014-01-17	rename SelectiveGenomeAmplification	Calvin Morrison