| Age | Commit message (Expand) | Author |
|---|---|---|
| 2014-01-29 | Limited number of markers in marker regression result table to•••those with a lod score > 2 Did some work towards adding the colored backgrounds to chromosome areas in the manhattan plot Changed the last two chromosomes for human manhattan plots to X and X/Y Started work on writing a script that can independently run the pyLMM code and store the results in redis | Zachary Sloan |
| 2014-01-24 | Added natural sort to sort the index column for the sample data in•••the trait page Hid the Quick Search on the index page until it is working well. Started writing a file to run the pyLMM code in the background to avoid memory issues/timing out | Zachary Sloan |
| 2014-01-23 | Histogram is working•••Fixed some bug with generating the manhattan plot for the HLC data set | Zachary Sloan |
| 2014-01-03 | Wrote some code for the histogram figure•••Changed some code in dataset to try and track down the issue with Amelie's file | Zachary Sloan |
| 2013-12-30 | Fixed issue where box plots initially appeared below the bar chart•••instead of in the second tab In the process of trying to fix the genofile to json parser so we can map Amelie's rat data In the process of having the color of bars in the bar chart "follow" them when they are resorted. | Zachary Sloan |
| 2013-12-05 | Interval map graph now works properly•••Tried to export trait data for "color by trait" function | Zachary Sloan |
| 2013-09-13 | Added file that will convert genofiles to plink ped/map files | Zachary Sloan |
| 2013-08-15 | Removed the markers with no variance (and thus no p-values) from the•••manhattan plot | Zachary Sloan |
| 2013-08-14 | Made some changes related to getting marker regression working for•••some datasets | Zachary Sloan |
| 2013-08-07 | Fixed things with the dataset dropdowns and mRNA datasets•••Improved the templates for a couple pages related to changing user password, etc | Zachary Sloan |
| 2013-07-30 | Just added some print statements to debug an issue with LMM code•••Also added some to notes | Zachary Sloan |
| 2013-07-23 | Fixed a couple issues with he quick_search_table.py script•••Added notes on using percona to optimise mysql to gn_installation_notes.txt Started moving "get_trait_data" to DataSet since it is the same regardless of the particular DataSet subclass (PhenotypeDataSet, MrnaAssayDataSet, etc) | Zachary Sloan |
| 2013-07-18 | Added Amelie's rat data genotypes•••Got human mapping mostly working Fixed dataset dropdown menus | Zachary Sloan |
| 2013-05-31 | Fixed the location column for the quick search page•••Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet) | Zachary Sloan |
| 2013-05-09 | Just added some print statements so I can show matrix/vector•••shapes to Tony | Zachary Sloan |
| 2013-05-02 | Got quick search code running (but not displaying properly)•••Code that processes subset of snps works, in process of putting into a class | Zachary Sloan |
| 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 st...•••Continued work on file that processes each individual chunk of the snp iterator/plink input | Zachary Sloan |
| 2013-04-24 | Began writing code that writes some objects used in LMM to redis•••and writes/reads eachitem in the plink_input | Zachary Sloan |
| 2013-04-23 | Created file correlation_plot.py for the correlation scatterplot•••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 | Zachary Sloan |
| 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•••we might decide to store it differently | Zachary Sloan |
| 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•••for HLC datasets Still need to read in file | Zachary Sloan |
| 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•••chunks algorithms' accuracy/speed | Zachary Sloan |
| 2013-04-17 | Wrote code that tests the effectiveness of the function that divides a•••list into a given number of chunks | Zachary Sloan |
| 2013-04-17 | Fixed small issue with the divide_into_chunks function•••that caused one too many chunks to be created | Zachary Sloan |
| 2013-04-16 | Wrote functions that divide a list into a specified number of chunks•••(to be used on the list of snps for the LMM code) | Zachary Sloan |
| 2013-04-16 | Checking in before making some changes | Zachary Sloan |
| 2013-04-16 | Put most of the code calculating human association statistics in•••lmm.py into a separate function | Zachary Sloan |
| 2013-04-09 | Nick's code works fine with human data•••Added option to limit results based on lod score (which also changes the y-axis of the plot) | Zachary Sloan |
| 2013-04-05 | Loading bar now correctly shows the time to completion•••and the code seems to run correctly | Zachary Sloan |
| 2013-04-05 | Got Nick's code working with the MDP datasets under the BXD group,•••but with only BXD strains | Zachary Sloan |
| 2013-04-02 | Finished adding code that uses the plink genotype data if•••a human dataset and json data if any other species | Zachary Sloan |
| 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•••table, but will need to check later to make sure | Zachary Sloan |
| 2013-03-26 | Just checking in code while in the process of trying to get•••the quick search working properly | Zachary Sloan |
| 2013-03-22 | Removed zach_settings.py from git tracking•••Changed mysql password as a result of it being up on git before | Zachary Sloan |
| 2013-03-21 | Did some work towards getting Nick's code working with our plink•••human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot | Zachary Sloan |
| 2013-03-19 | In the process of trying to use Nick's pylmmKinship.py code to•••precompute the kinship matrix for the human datasets we have plink .bed genotype data for | Zachary Sloan |
| 2013-03-19 | Added Nick's input.py file which uses plink .ped files as input•••for his pylmm code | Zachary Sloan |
| 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•••Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code | Zachary Sloan |
| 2013-03-07 | Created file temp_data to store data related to progress•••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 | Zachary Sloan |
| 2013-03-06 | Stored percent of calculate_kinship function completion in•••variable | Zachary Sloan |
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