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2013-06-11Put trait info for correlation results page into a dictionary insteadLei Yan
of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-30Rewrote some code in get_trait_info in dataset.pyLei Yan
Added spearman correlation to show_corr_results and template
2013-05-28Have correlation values appearing in a table in the templateLei Yan
Use scipy to calculate pearson correlation instead of old GN code
2013-05-23Worked on rewriting the function in data_set.py that gets the sampleLei Yan
values for each trait
2013-05-23Changed the way the query that gets sample ids is generatedLei Yan
2013-05-23Now calculates correlation values for traits, but not yet in templateLei Yan
2013-05-08Worked on correlation pageLei Yan
Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-04-30Changed path to log fileLei Yan
Added server port to configuration file
2013-04-23Created file correlation_plot.py for the correlation scatterplotZachary 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
2013-04-19Fixed the issue with the x-axis coordinates for marker regression plotZachary Sloan
2013-04-18The plink_input is split into chunks that are stored in temp_data, butZachary Sloan
we might decide to store it differently
2013-04-18LMM code now reads in gzipped pickled plink snp iterator objectZachary Sloan
2013-04-18input file is now loaded by pickleZachary Sloan
2013-04-17Created file with pickled SNPIterator (from input.py) dataZachary Sloan
for HLC datasets Still need to read in file
2013-04-17Added a benchmark for running the chunks code on the list of snpsZachary Sloan
2013-04-17Renamed chunk_test.py to chunks.pyZachary Sloan
2013-04-17Updated chunk_test.pyZachary Sloan
2013-04-17Added chunk_test.py which compared my/ and sam's split intoZachary Sloan
chunks algorithms' accuracy/speed
2013-04-17Wrote code that tests the effectiveness of the function that divides aZachary Sloan
list into a given number of chunks
2013-04-17Fixed small issue with the divide_into_chunks functionZachary Sloan
that caused one too many chunks to be created
2013-04-16Wrote functions that divide a list into a specified number of chunksZachary Sloan
(to be used on the list of snps for the LMM code)
2013-04-16Checking in before making some changesZachary Sloan
2013-04-16Put most of the code calculating human association statistics inZachary Sloan
lmm.py into a separate function
2013-04-11Fixed a bug with quick_search_table.pyZachary Sloan
Edited generate_probesetfreeze_file.py to try running it on the dataset with incorrect regression lines
2013-04-10Created template for quick search pageZachary Sloan
Fixed a couple bugs with quick_search_table.py
2013-04-09Have quick search working for phenotypesZachary Sloan
2013-04-09Nick's code works fine with human dataZachary Sloan
Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-04-05Loading bar now correctly shows the time to completionZachary Sloan
and the code seems to run correctly
2013-04-05Made change to nginx config file that seems to have fixed theZachary Sloan
504 gateway timeout issue with the human datasets
2013-04-05Got Nick's code working with the MDP datasets under the BXD group,Zachary Sloan
but with only BXD strains
2013-04-05Made changes to get pylmm code working with HMDP datasetsZachary Sloan
2013-04-02Finished adding code that uses the plink genotype data ifZachary Sloan
a human dataset and json data if any other species
2013-04-02Committing before splitting code that runs pylmm with plink filesZachary Sloan
and code that runs it with json
2013-04-02pylmm code is running for human data (plink .bed genotype files)Zachary Sloan
2013-03-28quick_search_table.py seems to be running OK for the PublishXRefZachary Sloan
table, but will need to check later to make sure
2013-03-28quick_search_table.py now seems to run correctly for ProbeSetXRefZachary Sloan
rows
2013-03-28Committing before putting quick_search_table code in classesZachary Sloan
2013-03-27Got quick_search_table.py to a point where it runs; willZachary Sloan
know tomorrow whether it ran correctly or not
2013-03-27Worked on trying to get results for quick search to displayZachary Sloan
2013-03-26Continued working on quick_search_table.py, which now getsZachary Sloan
all of the terms from the ProbeSet table to be included in the quick search
2013-03-26Created quick_search_table.py to create table with all of theZachary Sloan
information needed for the the quick search features (which searches across all datasets)
2013-03-26Just checking in code while in the process of trying to getZachary Sloan
the quick search working properly
2013-03-22Began creating templates for login/registrationZachary Sloan
2013-03-22Added secure_server.pyZachary Sloan
Updated notes.txt
2013-03-22Removed zach_settings.py from git trackingZachary Sloan
Changed mysql password as a result of it being up on git before
2013-03-21Did some work towards getting Nick's code working with our plinkZachary Sloan
human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot
2013-03-19In the process of trying to use Nick's pylmmKinship.py code toZachary Sloan
precompute the kinship matrix for the human datasets we have plink .bed genotype data for
2013-03-19Added Nick's input.py file which uses plink .ped files as inputZachary Sloan
for his pylmm code
2013-03-19Searches work for the full access human datasets with mRNA assayZachary Sloan
searches, and the trait page can be loaded Need to get marker regression page working with human data now
2013-03-15Began work with implementing general searchZachary Sloan
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