aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base/data_set.py
AgeCommit message (Expand)Author
2014-05-05Committing a bunch of changes related to integrating GEMMA and...adding the correlation matrix page Zachary Sloan
2014-01-30Most of the work is done towards running lmm.py from the command line...and storing the results in redis Zachary Sloan
2014-01-29Limited 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
2014-01-23Histogram is working...Fixed some bug with generating the manhattan plot for the HLC data set Zachary Sloan
2014-01-03Wrote some code for the histogram figure...Changed some code in dataset to try and track down the issue with Amelie's file Zachary Sloan
2013-11-26Made some progress towards getting the traits inside a collection to display ...Zachary Sloan
2013-11-25Got the interval mapping results into a tableZachary Sloan
2013-10-25Began working on color coding bar chart by extra attributesZachary Sloan
2013-10-15Changed templates to call the header macro...Correlation page now works with Non-BXD (or whatever group) or All Samples options Zachary Sloan
2013-10-11Merge /home/lei/gene...Conflicts: wqflask/maintenance/quick_search_table.py Zachary Sloan
2013-10-10Almost have correlation working for non-primary strain/group...There's just some issue with parents/f1s not being included if you select non-BXD (or whatever the group is). All Samples, however does work. Lei Yan
2013-10-09Improved some of the code related to the correlation page...For example, changed the two functions getting gene symbols and ids for a dataset into one function that can take a column name as a parameter Lei Yan
2013-10-08Literature correlation works when it is selected as the sorted...correlation type (that is, when it is run again all traits in a database) Added a function to data_set.py that gets all the gene_ids in the data set. Not sure if having a separate function for getting the gene_ids and another for getting the gene symbols makes sense. Lei Yan
2013-10-08Did some work with interval mapping page; will use qtl reaper to do...the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl Zachary Sloan
2013-09-24Did some work towards doing the tissue correlation for all traits...in a dataset (in order to sort by tissue correlation instead of sample correlation). root
2013-08-21Just removed a couple print statementsZachary Sloan
2013-08-15Removed the markers with no variance (and thus no p-values) from the...manhattan plot Zachary Sloan
2013-08-13Added several test files and the file with the class that...they import (browser_test.py) Zachary Sloan
2013-08-07Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user password, etc Zachary Sloan
2013-08-02Fixed a bug related to groups with genofiles (not sure if it makes sense...for them not to have genofiles yet) Zachary Sloan
2013-07-30Just added some print statements to debug an issue with LMM code...Also added some to notes Zachary Sloan
2013-07-23Fixed 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
2013-07-19Finished integrating code that reads sample list from geno files...withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page Zachary Sloan
2013-07-19Created file gen_group_samplelists that iterates through all genofiles...and builds each groups' samplelist Zachary Sloan
2013-07-16Wrote code that can get a dataset's type for every single GN...dataset; previously we could not view traits in datasets that were not in the DBType table in the database Zachary Sloan
2013-06-27Created a group manager page where user administrators can create...groups of datasets to give/add read privileges to Zachary Sloan
2013-06-26Moved code creating DataSets object to a function in dataset.py...Added caching to creating DataSets object Zachary Sloan
2013-06-26Got code that creates DataSets object running...Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases Zachary Sloan
2013-06-25Added DataSets class to dataset.py that will be used to create list of...confidential datasets Zachary Sloan
2013-06-21Fixed bug where cursor was still being used in queryZachary Sloan
2013-06-19Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask...Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page Zachary Sloan
2013-06-13Fixed issue where too much memory was used as a result of creating a...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 Lei Yan
2013-06-12Fixed a couple issues with the template that caused the...regular search results and show trait page to not display Zachary Sloan
2013-06-11Put trait info for correlation results page into a dictionary instead...of storing list of GeneralTrait objects Added print statements to track memory usage Lei Yan
2013-05-30Rewrote some code in get_trait_info in dataset.py...Added spearman correlation to show_corr_results and template Lei Yan
2013-05-28Have correlation values appearing in a table in the template...Use scipy to calculate pearson correlation instead of old GN code Lei Yan
2013-05-23Worked on rewriting the function in data_set.py that gets the sample...values for each trait Lei Yan
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
2013-05-09Just added some print statements so I can show matrix/vector...shapes to Tony Zachary Sloan
2013-05-08Worked on correlation page...Wrote function in dataset.py that gets all the traits in a dataset and their sample values Lei Yan
2013-04-09Nick'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
2013-04-05Made changes to get pylmm code working with HMDP datasetsZachary Sloan
2013-04-02Committing before splitting code that runs pylmm with plink files...and code that runs it with json Zachary Sloan
2013-04-02pylmm code is running for human data (plink .bed genotype files)Zachary Sloan
2013-03-19Searches work for the full access human datasets with mRNA assay...searches, and the trait page can be loaded Need to get marker regression page working with human data now Zachary Sloan
2013-03-12Got cashing working with pickleZachary Sloan
2013-03-07Progress 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
2013-03-02Created generate_probesetfreeze_file to create the..."probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with Zachary Sloan
2013-02-14Have marker regression results displaying as a scatterplot (just the points)...using d3.js Zachary Sloan