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2013-06-19Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columnsLei Yan
in the correlation page weren't displaying
2013-06-19Merge branch 'flask' of git://github.com/zsloan/genenetwork into flaskLei Yan
Conflicts: wqflask/base/data_set.py
2013-06-19:Merge git://github.com/zsloan/genenetwork into flaskLei Yan
Conflicts: wqflask/requirements.txt
2013-06-19Changed QTL parameter name to "get_qtl_info" on trait.py andLei Yan
other places it's called, like search_results.py Added other trait info fields to correlation results page
2013-06-13Fixed issue where too much memory was used as a result of creating aLei Yan
dataset object for each trait in the correlation results Added new fields/columns for each trait in the correlation result table (max LRS, max LRS location, mean expression) Fixed error if trait doesn't have these fields
2013-06-13Put the template html for the quick search page when all trait typesZachary Sloan
are displayed in a separate file that is included in quick_search.html
2013-06-12Fixed a couple issues with the template that caused theZachary Sloan
regular search results and show trait page to not display
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
2013-05-31Fixed the location column for the quick search pageZachary Sloan
Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet)
2013-05-30Rewrote 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
2013-05-21Added caching to the search page (for both regular and quick searckes)Zachary Sloan
2013-05-17Did a little work with quick search pageZachary Sloan
2013-05-16Made the first level of quick search tabs species, followed byZachary Sloan
trait type (was the opposite before Rob commented on it earlier today)
2013-05-09Just added some print statements so I can show matrix/vectorZachary Sloan
shapes to Tony
2013-05-08Merge branch 'flask' of git://github.com/leiyan/genenetwork into flaskZachary Sloan
2013-05-08Worked on correlation pageLei Yan
Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-05-07Made some progress adding species/group tabs to the quick search result page toZachary Sloan
make the results easier to navigate
2013-05-02Got quick search code running (but not displaying properly)Zachary Sloan
Code that processes subset of snps works, in process of putting into a class
2013-04-30Merge branch 'flask' of git://github.com/leiyan/genenetwork into flaskZachary Sloan
2013-04-30Changed path to log fileLei Yan
Added server port to configuration file
2013-04-30Did a little with correlation_plot.pyZachary Sloan
2013-04-26Added 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
2013-04-24Began writing code that writes some objects used in LMM to redisZachary Sloan
and writes/reads eachitem in the plink_input
2013-04-24Added original pylintrcZachary Sloan
2013-04-24Checking in quick_search_table.py before using pylinZachary Sloan
2013-04-24Fixed issue with the part of quick_search_table.py that loads phenotype traitsZachary Sloan
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
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