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path: root/wqflask/base/data_set.py
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2013-10-08Literature correlation works when it is selected as the sortedLei Yan
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.
2013-09-24Did some work towards doing the tissue correlation for all traitsroot
in a dataset (in order to sort by tissue correlation instead of sample correlation).
2013-08-21Just removed a couple print statementsZachary Sloan
2013-08-15Removed the markers with no variance (and thus no p-values) from theZachary Sloan
manhattan plot
2013-08-13Added several test files and the file with the class thatZachary Sloan
they import (browser_test.py)
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-08-02Fixed a bug related to groups with genofiles (not sure if it makes senseZachary Sloan
for them not to have genofiles yet)
2013-07-30Just added some print statements to debug an issue with LMM codeZachary Sloan
Also added some to notes
2013-07-23Fixed a couple issues with he quick_search_table.py scriptZachary Sloan
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)
2013-07-19Finished integrating code that reads sample list from geno filesZachary Sloan
withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-19Created file gen_group_samplelists that iterates through all genofilesZachary Sloan
and builds each groups' samplelist
2013-07-16Wrote code that can get a dataset's type for every single GNZachary Sloan
dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-06-27Created a group manager page where user administrators can createZachary Sloan
groups of datasets to give/add read privileges to
2013-06-26Moved code creating DataSets object to a function in dataset.pyZachary Sloan
Added caching to creating DataSets object
2013-06-26Got code that creates DataSets object runningZachary Sloan
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
2013-06-25Added DataSets class to dataset.py that will be used to create list ofZachary Sloan
confidential datasets
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 flaskZachary Sloan
Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation 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
2013-06-12Fixed 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
2013-05-30Rewrote 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
2013-05-09Just added some print statements so I can show matrix/vectorZachary Sloan
shapes to Tony
2013-05-08Worked on correlation pageLei Yan
Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-04-09Nick'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
2013-03-12Got 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
2013-02-14Have 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
2013-01-31Changed fd to kw in search_results.py, commented out some linesZachary Sloan
related to fd
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
2013-01-03Began 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
2012-12-06Added 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
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