| Age | Commit message (Expand) | Author |
|---|
| 2016-04-20 | [PATCH 027/100] Introduce tools.locate | Pjotr Prins |
| 2016-04-20 | [PATCH 026/100] Introducing cached values PYLMM_COMMAND,... GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR
| Pjotr Prins |
| 2016-04-20 | Introducing TEMPDIR | pjotrp |
| 2016-04-20 | [PATCH 024/100] Sanitizing file handling | Pjotr Prins |
| 2016-04-20 | [PATCH 023/100] WIP fixing all paths | Pjotr Prins |
| 2016-04-20 | [PATCH 018/100] Find external tools: refactored code to work with GNU Guix | Pjotr Prins |
| 2016-04-07 | SNP Track option should now work for GN1 mapping figure...Fixed typo in show_trait html that caused the p-value slider to not work for correlations
| zsloan |
| 2016-04-06 | Permutations (suggestive/significant lines, legend, and histogram) should now......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
| zsloan |
| 2015-11-09 | Fixed issue that caused mapping to not work; for some reason the path to pylm... | zsloan |
| 2015-07-09 | Mapping methods now check for existing genotype files....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
| zsloan |
| 2015-06-29 | Merge pull request #72 from lomereiter/issue69...Fixes #69 | zsloan |
| 2015-06-29 | Merge pull request #77 from lomereiter/fix_sql...SQL security fixes | zsloan |
| 2015-06-26 | Fixed bug where mapping results sometimes wouldn't display. This would occur...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.
| zsloan |
| 2015-06-18 | removed unused function | Artem Tarasov |
| 2015-06-18 | add missing line to webqtlUtil | Artem Tarasov |
| 2015-05-12 | Add info to warning | pjotrp |
| 2015-05-12 | More elaborate handling of finding pylmm | Pjotr Prins |
| 2015-05-12 | Move path search into tools.py | pjotrp |
| 2015-05-11 | Moving pylmm out of the tree | pjotrp |
| 2014-08-12 | Fixed the scrollable data tables for the show trait page...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
| Zachary Sloan |
| 2014-07-18 | Added outlier highlighting...Changed order of tabs in statistics panel on trait page
Started working on heatmap
| Zachary Sloan |
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and...adding the correlation matrix page
| Zachary Sloan |
| 2014-02-27 | Began working on a TraitCollection.py file that will contain both the...object for logged in user collections and collections created by
anonymous users.
| Zachary Sloan |
| 2013-10-17 | Sample objects are now passed to js_data for drawing the correlation...scatter plot
| Lei Yan |
| 2013-10-11 | Merge /home/sam/gene | Lei Yan |
| 2013-10-07 | Worked on logins, session_ids, flash messages, etc. | Sam |
| 2013-09-13 | Merge https://github.com/zsloan/genenetwork...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
| Lei Yan |
| 2013-07-19 | Finished 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 |
| 2013-07-12 | Rewrote code related to getting the tissue correlation column to display...Created new files for mrna assay tissue data and commonly used
db query related functions
| Lei Yan |
| 2013-06-20 | Added file corr_result_helpers.py that includes the function that...normalizes the lists of sample values
| Zachary Sloan |
| 2013-06-19 | Merge 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 |
| 2013-06-13 | Fixed 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 |
| 2013-05-23 | Lots of changes around users | Sam |
| 2013-04-23 | Created file correlation_plot.py for the correlation scatterplot...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
| Zachary Sloan |
| 2013-04-18 | The plink_input is split into chunks that are stored in temp_data, but...we might decide to store it differently
| Zachary Sloan |
| 2013-04-17 | Created file with pickled SNPIterator (from input.py) data...for HLC datasets
Still need to read in file
| Zachary Sloan |
| 2013-04-05 | Loading bar now correctly shows the time to completion...and the code seems to run correctly
| Zachary Sloan |
| 2013-03-12 | Got cashing working with pickle | Zachary Sloan |
| 2013-03-07 | Have first 45% of progress bar working...Changed "threaded" to True in runserver.py; this fixed issue
related to getting progress bar to work
| Zachary Sloan |
| 2013-03-07 | Created file temp_data to store data related to progress...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
| Zachary Sloan |
| 2013-02-28 | Updated benchmark.py to aggregate run times when you run the...operation(s) multiple times
| Zachary Sloan |
| 2013-02-28 | Added benchmark.py that compares the time of various operations...and gives a report with the percent of total computation time
each takes
| Zachary Sloan |
| 2013-02-19 | Made lines for manhattan plot proportional to chromosome lengths | Zachary Sloan |
| 2013-01-31 | Changed reference to 'dataset_name' in keywords to 'dataset' to get...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
| Zachary Sloan |
| 2013-01-22 | Pushed through a few errors in getting the correlation page running | Zachary Sloan |
| 2013-01-18 | Renamed CorrelationPage.py to show_corr_results.py...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
| Zachary Sloan |
| 2012-09-27 | Worked on getting attributes in the SampleList object to display data properl... | Zachary Sloan |
| 2012-09-26 | Worked on implementing the extra attributes feature on the trait data page | Zachary Sloan |
| 2012-08-29 | Fixed so that outliers are now correctly highlighted | Zachary Sloan |
| 2012-08-28 | Various changes related to the webqtlCaseData object and the way values/varia... | Zachary Sloan |
