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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
2013-06-11Put 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
2013-04-17Created file with pickled SNPIterator (from input.py) dataZachary Sloan
for HLC datasets Still need to read in file
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)
2013-04-05Made changes to get pylmm code working with HMDP datasetsZachary Sloan
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
2013-03-19Searches 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
2013-03-12Added the script generating probesetfreeze data matrix filesZachary Sloan
The script was created to regenerate a bad file for Evan
2013-03-12Got cashing working with pickleZachary Sloan
2013-03-07Progress bar is now completely workingZachary Sloan
Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code
2013-03-02Created generate_probesetfreeze_file to create theZachary Sloan
"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with
2013-02-22Added some to notesZachary Sloan
2013-02-14Have marker regression results displaying as a scatterplot (just the points)Zachary Sloan
using d3.js
2013-02-13Fixed some bugs related to getting the marker regression page workingZachary Sloan
with Nick's code
2013-02-12Edited marker_regression.py and data_set.py to store the p-valuesZachary Sloan
and their corresponding markers to be used in the table of qtl results and other figures
2013-02-07Added code to marker_regression.py that creates the numpy arrays toZachary 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
2013-01-31Changed fd to kw in search_results.py, commented out some linesZachary Sloan
related to fd
2013-01-25Fixed a few bugs while trying to get the code running on the new serverZachary Sloan
2013-01-18Renamed CorrelationPage.py to show_corr_results.pyZachary Sloan
Worked with correlation code; got to the code that begins to do the actual correlations Created a function "get_dataset_and_trait" in the new file "helper_functions.py" because the code initializing the dataset and trait objects was repeated in multiple places
2013-01-08Created IndChromosome class in species.py and wrote functions forZachary Sloan
chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugsZachary Sloan
Added a couple utility functions to the Chromosomes class in species.py
2013-01-03Began working on marker_regression.py and created Chromosomes classZachary Sloan
in species.py
2013-01-03Created template for marek regression page and made the compute button directZachary Sloan
to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-18Created new file species.py and species class object TheSpeciesZachary Sloan
Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests
2012-12-07Got basic statistics in show_trait to display the correct numberZachary Sloan
of samples for each group Got show_trait page to display for genotype traits
2012-12-06Added minimum/maximum to basic statistics tableZachary Sloan
Continued bug-shooting related to getting show_trait running with phenotype traits
2012-12-06Got show_trait running again for MrnaAssay traitsZachary Sloan
2012-12-06Made many small changes to show_trait/data_set/search_results/trait toZachary Sloan
remove use of the formData object and cursor
2012-12-05Renamed webqtlTrait.py to trait.pyZachary Sloan
Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough)
2012-12-05Continued to make changes related to getting rid of cursor/db_connZachary Sloan
and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again
2012-12-04Changed parser to allow quotes (i.e. name="rw williams")Zachary Sloan
Renamed webqtlTrait to GeneralTrait and began rewriting parts Changed database code in many places to use simple sqlalchemy
2012-12-04Began changing references to cursor/db_conn to use sqlalchemyZachary Sloan
Wrote function for phenotype author searches
2012-11-30Added example of escaping strings now that trasitioning to simple SQLAlchemyZachary Sloan
2012-11-30Started switching to using basic sqlalchemy to handle db connection/queriesZachary Sloan
Began fixing bugs related to this fix, still in progress
2012-11-29Changed a number of variables (riset to group, db to dataset)Zachary Sloan
Put most of the code for cisLRS and transLRS searches into the class CisTransLrsSearch (might change this name to something else later) Simplified escape code for searches in do_search.py Got search_results working again after some changes
2012-11-28Made some small changes to get code working for genotype searchesZachary Sloan
2012-11-27Created subclass for each main data set type and moved the codeZachary Sloan
for getting trait info that was in search_results.py into its respective class Renamed webqtlDataset to DataSet/create_dataset in webqtlTrait.py, webqtlDatabaseFunction.py, and CorrelationPage.py Got search page running again for mRNA assay data sets with these changes
2012-11-27Renamed webqtlDataSet.py to data_set.pyZachary Sloan
Renamed the class webqtlDataset to DataSet Finished cisLRS and transLRS search types in d_search.py Fixed parent/f1 issue in show_trait.py
2012-10-30Worked on search_result.py code related to adding clause item to queriesZachary Sloan
Continued work on redesigning the trait data page design
2012-10-26Got search page working for mice with a single gene searchZachary Sloan
2012-10-25Worked on search page code; got to the part that actually does the searchZachary Sloan
Renamed RISet and cross to "group" throughout webqtlDataset.py and search_results.py
2012-10-24Now builds json datastructure for menus correctlyZachary Sloan
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