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

Age	Commit message (Collapse)	Author
2013-03-18	Merge remote-tracking branch 'origin/master'	Calvin

2013-03-18	don't try and force 2.7, it might not work	Calvin

2013-03-18	remove checking, seems like the sml code isn't returning sane values	mutantturkey

2013-03-16	add return code checking	mutantturkey

2013-03-16	use is_compressed	mutantturkey

2013-03-16	we don't need a kmer file anymore :-)	mutantturkey

2013-03-15	eliminated the need for Nmers.txt:-)	Calvin

2013-03-15	added generate_kmers to the makefile	Calvin

2013-03-15	delete binaries	Calvin

2013-03-15	nbc added	Calvin

2013-03-15	specify python2.7	Calvin

2013-03-15	specify python 2.7 in multifasta	Calvin

2013-03-15	updated multifasta_to_otu to is_compressed	Calvin

2013-03-14	formatting fixes and renamed isCompressed to is_compressed	Calvin

2013-03-14	fix automatically creating output directory	Calvin

2013-03-14	fix multifasta_to_otu to use proper function names... need to get some ↵	Calvin
	automatic unit testing going or something
2013-03-14	fixed an incorrect namespace	Calvin

2013-03-14	get rid of OS checks for count, assume it is called count-kmers	Calvin

2013-03-14	re-add the kmer filename checK	Calvin

2013-03-13	fix bad old commit	Calvin

2013-03-13	added multi_fasta_otu to cli.markdown	Calvin

2013-03-13	added matlab markdown and edited cli	Calvin

2013-03-13	added setup.py for python quikr module	Calvin

2013-03-13	updated makefile to install nbc properly and python properly.	Calvin

2013-03-12	initial commit of some documentation	Calvin

2013-03-12	removed multifasta's py extension, modified the --help argument output for ↵	Calvin
	quikr_train
2013-03-11	removed documented matlab, add bare makefile	Calvin

2013-03-11	move python stuff to python directory	Calvin

2013-03-11	adding matlab code	Calvin

2013-03-08	moving some stuff	Calvin

2013-03-08	fix quikr_train to work with updated quikr module	mutantturkey

2013-03-08	convert into a module, rename out functions so all quikr functions are ↵	mutantturkey
	withing quikr.function name
2013-03-08	fix quikr	mutantturkey

2013-03-08	fix multifasta_to_otu	mutantturkey

2013-03-07	starting to modularize	Calvin

2013-03-07	minor formatting cleanup	Calvin

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

2013-03-07	added gzip compression support	Calvin

2013-03-07	Check if file is compressed	Calvin

2013-03-06	removed debugging statements	Calvin

2013-03-06	do the matrix rotations and manipulations in quikr_train instead of quikr	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
2013-03-05	simplify generate_kmers.py	Calvin

2013-03-05	Added generate_kmers.py	Calvin
	This little script will output all the possible kmer permutations to stdout. The only input is the kmer length desired. Here are some examples. output 2mers ./generate_kmers.py 2 > 2mers.py output N-mers up to 6 with a bit of bash-foo for i in `seq 6`; do ./generate_kmers.py $i > ${i}mers.txt; done;
2013-02-28	use the load from file instead of calling it directly, should work now.	Calvin

2013-02-27	working on the iterators	Calvin

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