quikr.git - Quikr - a bio classifier based on NNLS

Age	Commit message (Collapse)	Author
2013-03-08	moving some stuff	Calvin

2013-03-08	fix multifasta_to_otu	mutantturkey

2013-03-07	multifasta_to_otu.py support for compression	Calvin

2013-03-06	Cleanups and refactoring	Calvin
	* Only do one check for output_directory by combining statements * rename output to number_of_reads * get rid of useless comment
2013-03-06	fixed index	Calvin

2013-03-06	formatting cleanups, removed unused import, deleted unused lines	Calvin

2013-03-05	Added OTU table output and grep parsing	Calvin
	A giant batch commit. Sorry! * OTU table output * results are still different from matlab * sample names still have suffix * otherwise should be ok * only return rows which sum up to greater than zero (ie non empty) * Use grep instead of BIOseq because it is a lot faster to count our sequences this way. * re-enable our pool process management * refactor and rename records to headers * refactor final_output to output
2013-02-27	working on the iterators	Calvin

2013-02-27	Create a dictionary of our trained matrix id's	Calvin

2013-02-27	Write the comments in for the work to be done	Calvin
	Comment first, write code later! Also I fixed an erroneous space that really didn't need to be there. Laid down the import for biopyton. Created the basic iteration through our fasta files and added loading of fasta file titles through biopython
2013-02-27	Update multifasta_to_otu.py for new quikr function	Calvin
	* Removed an old comment from the quikr function * Load the trained matrix from multifasta main. * This will reduce load times as we only need to call it once
2013-02-26	changes	Calvin

2013-02-26	merge resolution	Calvin

2013-02-26	some upodates	Calvin

2013-02-26	iteratively loop through	mutantturkey

2013-02-25	fixed syntax mistake	Calvin

2013-02-25	initial commit, playing around with threading	mutantturkey