genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-05-31	Fixed the location column for the quick search page	Zachary Sloan
	Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet)
2013-05-09	Just added some print statements so I can show matrix/vector	Zachary Sloan
	shapes to Tony
2013-05-02	Got quick search code running (but not displaying properly)	Zachary Sloan
	Code that processes subset of snps works, in process of putting into a class
2013-04-30	Did a little with correlation_plot.py	Zachary Sloan

2013-04-26	Added file that checks how much time is added to a loop's runtime by print ↵	Zachary Sloan
	statements Continued work on file that processes each individual chunk of the snp iterator/plink input
2013-04-24	Began writing code that writes some objects used in LMM to redis	Zachary Sloan
	and writes/reads eachitem in the plink_input
2013-04-23	Created file correlation_plot.py for the correlation scatterplot	Zachary Sloan
	Reverted temp_data.py to previous version that doesn't include the "part" input (for chunks) Made change to lmm related to splitting main iterator into chunks Deleted a bunch of unnecessary commented out code from show_trait.py
2013-04-19	Fixed the issue with the x-axis coordinates for marker regression plot	Zachary Sloan

2013-04-18	The plink_input is split into chunks that are stored in temp_data, but	Zachary Sloan
	we might decide to store it differently
2013-04-18	LMM code now reads in gzipped pickled plink snp iterator object	Zachary Sloan

2013-04-18	input file is now loaded by pickle	Zachary Sloan

2013-04-17	Created file with pickled SNPIterator (from input.py) data	Zachary Sloan
	for HLC datasets Still need to read in file
2013-04-17	Added a benchmark for running the chunks code on the list of snps	Zachary Sloan

2013-04-17	Renamed chunk_test.py to chunks.py	Zachary Sloan

2013-04-17	Updated chunk_test.py	Zachary Sloan

2013-04-17	Added chunk_test.py which compared my/ and sam's split into	Zachary Sloan
	chunks algorithms' accuracy/speed
2013-04-17	Wrote code that tests the effectiveness of the function that divides a	Zachary Sloan
	list into a given number of chunks
2013-04-17	Fixed small issue with the divide_into_chunks function	Zachary Sloan
	that caused one too many chunks to be created
2013-04-16	Wrote functions that divide a list into a specified number of chunks	Zachary Sloan
	(to be used on the list of snps for the LMM code)
2013-04-16	Checking in before making some changes	Zachary Sloan

2013-04-16	Put most of the code calculating human association statistics in	Zachary Sloan
	lmm.py into a separate function
2013-04-09	Nick's code works fine with human data	Zachary Sloan
	Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-04-05	Loading bar now correctly shows the time to completion	Zachary Sloan
	and the code seems to run correctly
2013-04-05	Got Nick's code working with the MDP datasets under the BXD group,	Zachary Sloan
	but with only BXD strains
2013-04-02	Finished adding code that uses the plink genotype data if	Zachary Sloan
	a human dataset and json data if any other species
2013-04-02	pylmm code is running for human data (plink .bed genotype files)	Zachary Sloan

2013-03-28	quick_search_table.py seems to be running OK for the PublishXRef	Zachary Sloan
	table, but will need to check later to make sure
2013-03-26	Just checking in code while in the process of trying to get	Zachary Sloan
	the quick search working properly
2013-03-22	Removed zach_settings.py from git tracking	Zachary Sloan
	Changed mysql password as a result of it being up on git before
2013-03-21	Did some work towards getting Nick's code working with our plink	Zachary Sloan
	human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot
2013-03-19	In the process of trying to use Nick's pylmmKinship.py code to	Zachary Sloan
	precompute the kinship matrix for the human datasets we have plink .bed genotype data for
2013-03-19	Added Nick's input.py file which uses plink .ped files as input	Zachary Sloan
	for his pylmm code
2013-03-08	Caching is working for marker regression but really slowly	Zachary Sloan

2013-03-08	Refactored GWAS function in lmm.py	Zachary Sloan

2013-03-07	Progress bar is now completely working	Zachary Sloan
	Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code
2013-03-07	Created file temp_data to store data related to progress	Zachary Sloan
	of the marker regression calculations Storing progress of kinship matrix calculation in variable as portion of 45 (the rough percent of total marker regression calculation time
2013-03-06	Stored percent of calculate_kinship function completion in	Zachary Sloan
	variable
2013-02-28	Added benchmark.py that compares the time of various operations	Zachary Sloan
	and gives a report with the percent of total computation time each takes
2013-02-21	Add my_pylmm package	Zachary Sloan

2013-02-13	Got results displaying for BXD and fixed genofile_parser.py to work	Zachary Sloan
	for all of our genofiles
2013-02-12	Edited marker_regression.py and data_set.py to store the p-values	Zachary Sloan
	and their corresponding markers to be used in the table of qtl results and other figures
2013-02-08	Converted .geno files to json files and wrote code in marker_regression.py	Zachary Sloan
	that loads the json files, converts them into the relevant numpy arrays, and passes them into Nick's code (which is returning results that may or may not be correct, but is at least running)
2013-02-07	Added code to marker_regression.py that creates the numpy arrays to	Zachary Sloan
	pass to Nick's code and changed the prep_data.py code to operate on a list of phenotype values instead of a textfile with the values delimited
2013-02-06	Edited genofile_parser.py to go through all genofiles and convert	Zachary Sloan
	them to the format used by nick's code