| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2013-06-26 | Moved code creating DataSets object to a function in dataset.py | Zachary Sloan | |
| Added caching to creating DataSets object | |||
| 2013-06-26 | Got code that creates DataSets object running | Zachary 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 | |||
| 2013-06-25 | Added DataSets class to dataset.py that will be used to create list of | Zachary Sloan | |
| confidential datasets | |||
| 2013-06-21 | Fixed bug where cursor was still being used in query | Zachary Sloan | |
| 2013-06-19 | Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask | Zachary 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 | |||
| 2013-06-13 | Fixed issue where too much memory was used as a result of creating a | Lei 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 | |||
| 2013-06-12 | Fixed a couple issues with the template that caused the | Zachary Sloan | |
| regular search results and show trait page to not display | |||
| 2013-06-11 | Put trait info for correlation results page into a dictionary instead | Lei Yan | |
| of storing list of GeneralTrait objects Added print statements to track memory usage | |||
| 2013-05-30 | Rewrote some code in get_trait_info in dataset.py | Lei Yan | |
| Added spearman correlation to show_corr_results and template | |||
| 2013-05-28 | Have correlation values appearing in a table in the template | Lei Yan | |
| Use scipy to calculate pearson correlation instead of old GN code | |||
| 2013-05-23 | Worked on rewriting the function in data_set.py that gets the sample | Lei Yan | |
| values for each trait | |||
| 2013-05-23 | Changed the way the query that gets sample ids is generated | Lei Yan | |
| 2013-05-23 | Now calculates correlation values for traits, but not yet in template | Lei Yan | |
| 2013-05-09 | Just added some print statements so I can show matrix/vector | Zachary Sloan | |
| shapes to Tony | |||
| 2013-05-08 | Worked on correlation page | Lei Yan | |
| Wrote function in dataset.py that gets all the traits in a dataset and their sample values | |||
| 2013-04-09 | Nick's code works fine with human data | Zachary Sloan | |
| Added option to limit results based on lod score (which also changes the y-axis of the plot) | |||
| 2013-04-05 | Made changes to get pylmm code working with HMDP datasets | Zachary Sloan | |
| 2013-04-02 | Committing before splitting code that runs pylmm with plink files | Zachary Sloan | |
| and code that runs it with json | |||
| 2013-04-02 | pylmm code is running for human data (plink .bed genotype files) | Zachary Sloan | |
| 2013-03-19 | Searches work for the full access human datasets with mRNA assay | Zachary Sloan | |
| searches, and the trait page can be loaded Need to get marker regression page working with human data now | |||
| 2013-03-12 | Got cashing working with pickle | Zachary Sloan | |
| 2013-03-07 | Progress bar is now completely working | Zachary Sloan | |
| Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code | |||
| 2013-03-02 | Created generate_probesetfreeze_file to create the | Zachary Sloan | |
| "probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with | |||
| 2013-02-14 | Have marker regression results displaying as a scatterplot (just the points) | Zachary Sloan | |
| using d3.js | |||
| 2013-02-13 | Fixed some bugs related to getting the marker regression page working | Zachary Sloan | |
| with Nick's code | |||
| 2013-02-12 | Edited marker_regression.py and data_set.py to store the p-values | Zachary Sloan | |
| and their corresponding markers to be used in the table of qtl results and other figures | |||
| 2013-01-31 | Changed fd to kw in search_results.py, commented out some lines | Zachary Sloan | |
| related to fd | |||
| 2013-01-18 | Renamed CorrelationPage.py to show_corr_results.py | Zachary 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 | |||
| 2013-01-03 | Began working on marker_regression.py and created Chromosomes class | Zachary Sloan | |
| in species.py | |||
| 2013-01-03 | Created template for marek regression page and made the compute button direct | Zachary 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 | |||
| 2012-12-18 | Created new file species.py and species class object TheSpecies | Zachary 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 | |||
| 2012-12-06 | Added minimum/maximum to basic statistics table | Zachary Sloan | |
| Continued bug-shooting related to getting show_trait running with phenotype traits | |||
| 2012-12-06 | Got show_trait running again for MrnaAssay traits | Zachary Sloan | |
| 2012-12-06 | Made many small changes to show_trait/data_set/search_results/trait to | Zachary Sloan | |
| remove use of the formData object and cursor | |||
| 2012-12-05 | Renamed webqtlTrait.py to trait.py | Zachary 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) | |||
| 2012-12-05 | Continued to make changes related to getting rid of cursor/db_conn | Zachary Sloan | |
| and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again | |||
| 2012-12-04 | Changed 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 | |||
| 2012-12-04 | Began changing references to cursor/db_conn to use sqlalchemy | Zachary Sloan | |
| Wrote function for phenotype author searches | |||
| 2012-11-30 | Added example of escaping strings now that trasitioning to simple SQLAlchemy | Zachary Sloan | |
| 2012-11-30 | Started switching to using basic sqlalchemy to handle db connection/queries | Zachary Sloan | |
| Began fixing bugs related to this fix, still in progress | |||
| 2012-11-29 | Changed 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 | |||
| 2012-11-28 | Made some small changes to get code working for genotype searches | Zachary Sloan | |
| 2012-11-27 | Created subclass for each main data set type and moved the code | Zachary 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 | |||
| 2012-11-27 | Renamed webqtlDataSet.py to data_set.py | Zachary 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 | |||
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |