aboutsummaryrefslogtreecommitdiff
path: root/wqflask/utility
AgeCommit message (Collapse)Author
2016-04-20tools.py: add function locate_without_errorpjotrp
2016-04-20[PATCH 027/100] Introduce tools.locatePjotr Prins
2016-04-20[PATCH 026/100] Introducing cached values PYLMM_COMMAND,Pjotr Prins
GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR
2016-04-20Introducing TEMPDIRpjotrp
2016-04-20[PATCH 024/100] Sanitizing file handlingPjotr Prins
2016-04-20[PATCH 023/100] WIP fixing all pathsPjotr Prins
2016-04-20[PATCH 018/100] Find external tools: refactored code to work with GNU GuixPjotr Prins
2016-04-07SNP Track option should now work for GN1 mapping figurezsloan
Fixed typo in show_trait html that caused the p-value slider to not work for correlations
2016-04-06Permutations (suggestive/significant lines, legend, and histogram) should ↵zsloan
now work for both R/qtl and qtl reaper mapping. Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant
2015-11-09Fixed issue that caused mapping to not work; for some reason the path to ↵zsloan
pylmm was wrong
2015-07-09Mapping methods now check for existing genotype files.zsloan
Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory
2015-06-29Merge pull request #72 from lomereiter/issue69zsloan
Fixes #69
2015-06-29Merge pull request #77 from lomereiter/fix_sqlzsloan
SQL security fixes
2015-06-26Fixed bug where mapping results sometimes wouldn't display. This would occurzsloan
due to a chromosome (in this case the last) not having any markers. Improved the way plink gets its path/command to use a method similar to the one Pjotr used with pylmm. I'll also do this for the other mapping methods. Fixed issue where the Y axis would always say LOD score. It now says LRS for mapping methods that return LRS Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary) Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results in a new page. I had resolved every issue but the mapping javascript (lod_chart) not being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty sure that this is because js_data was inserted into the html after the page was loaded while the chart code ran immediately. I experimented with adding a short timeout to the mapping javascript and data table javascript, but while it worked for the table it did not work for the mapping figure. I don't know why this is.
2015-06-18removed unused functionArtem Tarasov
2015-06-18add missing line to webqtlUtilArtem Tarasov
2015-05-12Add info to warningpjotrp
2015-05-12More elaborate handling of finding pylmmPjotr Prins
2015-05-12Move path search into tools.pypjotrp
2015-05-11Moving pylmm out of the treepjotrp
2014-08-12Fixed the scrollable data tables for the show trait pageZachary Sloan
Added the option to display the rqtl results (and soon other mapping results) as either a manhattan plot or "interval map" style curve chart Removed a couple unnecessary javascript imports Changed the function in helper_functions.py that creates the trait and dataset objects, making it to where the trait object also gets qtl info Fixed color by trait after it was broken by the "scatterplot matrix" function
2014-07-18Added outlier highlightingZachary Sloan
Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-05-05Committing a bunch of changes related to integrating GEMMA andZachary Sloan
adding the correlation matrix page
2014-02-27Began working on a TraitCollection.py file that will contain both theZachary Sloan
object for logged in user collections and collections created by anonymous users.
2013-10-17Sample objects are now passed to js_data for drawing the correlationLei Yan
scatter plot
2013-10-11Merge /home/sam/geneLei Yan
2013-10-07Worked on logins, session_ids, flash messages, etc.Sam
2013-09-13Merge https://github.com/zsloan/genenetworkLei Yan
Resolved conflicts: wqflask/base/trait.py wqflask/wqflask/correlation/correlationFunction.py wqflask/wqflask/correlation/correlation_function.py wqflask/wqflask/correlation/correlation_functions.py wqflask/wqflask/correlation/show_corr_results.py
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
2013-07-12Rewrote code related to getting the tissue correlation column to displayLei Yan
Created new files for mrna assay tissue data and commonly used db query related functions
2013-06-20Added file corr_result_helpers.py that includes the function thatZachary Sloan
normalizes the lists of sample values
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
2013-05-23Lots of changes around usersSam
2013-04-23Created file correlation_plot.py for the correlation scatterplotZachary Sloan
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
2013-04-18The plink_input is split into chunks that are stored in temp_data, butZachary Sloan
we might decide to store it differently
2013-04-17Created file with pickled SNPIterator (from input.py) dataZachary Sloan
for HLC datasets Still need to read in file
2013-04-05Loading bar now correctly shows the time to completionZachary Sloan
and the code seems to run correctly
2013-03-12Got cashing working with pickleZachary Sloan
2013-03-07Have first 45% of progress bar workingZachary Sloan
Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work
2013-03-07Created file temp_data to store data related to progressZachary Sloan
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
2013-02-28Updated benchmark.py to aggregate run times when you run theZachary Sloan
operation(s) multiple times
2013-02-28Added benchmark.py that compares the time of various operationsZachary Sloan
and gives a report with the percent of total computation time each takes
2013-02-19Made lines for manhattan plot proportional to chromosome lengthsZachary Sloan
2013-01-31Changed reference to 'dataset_name' in keywords to 'dataset' to getZachary Sloan
page to work, but will change all references to the dataset name to 'dataset_name' in future to avoid confusion between the dataset name and the actual dataset object
2013-01-22Pushed through a few errors in getting the correlation page runningZachary 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
2012-09-27Worked on getting attributes in the SampleList object to display data ↵Zachary Sloan
properly, changed SampleList from an object list to object
2012-09-26Worked on implementing the extra attributes feature on the trait data pageZachary Sloan
2012-08-29Fixed so that outliers are now correctly highlightedZachary Sloan