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

Age	Commit message (Collapse)	Author
2014-07-16	add ifle	Calvin Morrison

2014-07-16	work on filters	Calvin Morrison

2014-07-03	fix that bug yo	Calvin Morrison

2014-06-25	make that a float	Calvin Morrison

2014-06-25	really reduce memory usage of select_mers.py	Calvin Morrison

2014-05-20	score regardless	Calvin Morrison

2014-05-20	fix div by zero	Calvin Morrison

2014-04-23	simplify select_mers.py	Calvin Morrison

2014-04-20	force bash on lock	Calvin Morrison

2014-04-18	force 2.7	Calvin Morrison

2014-04-14	keep asking for files if they don't exist, filter melting temperature with ↵	Calvin Morrison
	updated function
2014-04-14	added new stuff for filter melting temperature	Calvin Morrison

2014-04-14	don't use strstream, use kmer_locations	Calvin Morrison

2014-04-14	mkdir on lock claim	Calvin Morrison

2014-04-08	more docs and add strand	Calvin Morrison

2014-04-08	add lock	Calvin Morrison

2014-04-08	update arg info	Calvin Morrison

2014-04-07	tabular output	Calvin Morrison

2014-04-07	working output full genome.py	Calvin Morrison

2014-04-07	fix stream counting so it doesn't count over	Calvin Morrison

2014-04-07	initial commit of output_full_genome.py	Calvin Morrison

2014-04-07	add genome length	Calvin Morrison

2014-04-07	+x average_binding	Calvin Morrison

2014-04-07	fix reverse counts and output genome length	Calvin Morrison

2014-04-02	add exit codes	Calvin Morrison

2014-04-01	remove a debug line	Calvin Morrison

2014-04-01	add feature to read from previously scored all-scores file, clean up code as ↵	Calvin Morrison
	well
2014-04-01	check exit status and more error checking in check_feasilbe	Calvin Morrison

2014-03-31	fix bug in using combination file. this closes #18	Calvin Morrison

2014-03-31	add UI for scorign func, update doc and varaibles	Calvin Morrison

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

2014-03-31	add custom scoring	Calvin Morrison

2014-03-31	proper sizes with custom mers	Calvin Morrison

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

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

2014-03-27	Scoring all mer combinations from a file with a -m	Calvin Morrison

2014-03-27	improve output, add number of primers in first colum. this closes #12	Calvin Morrison

2014-03-27	move stuff around	Calvin Morrison

2014-03-27	Add 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
2014-03-26	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

2014-03-26	use float	Calvin Morrison

2014-03-25	Score mer statistics. This closes #6	Calvin Morrison

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

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