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path: root/wqflask/utility/tools.py
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2017-01-26GEMMA now works with CFW data (had to update where it looks for the input ↵zsloan
files and how it writes the phenotype file) Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results
2016-10-11Merge branch 'pjotr-gn2' into testingPjotr Prins
2016-10-09Add version informationPjotr Prins
2016-10-07Make sure JS path existsPjotr Prins
2016-10-07Changed error outputPjotr Prins
2016-10-07Saner handling of TMPDIR and TEMPDIRPjotr Prins
Throw error when TMPDIRs are not writable
2016-10-03Config: supporting JSON OVERRIDESPjotr Prins
2016-10-03Debug: sanitize some outputPjotr Prins
2016-09-25Make sure MAPPING_PATH existsPjotr Prins
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-09-10Support for running maintenance scripts so they can pick up all webserver ↵Pjotr Prins
settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
2016-06-24Log: and document SQL callsPjotr Prins
2016-06-23Logger: improved loggingPjotr Prins
2016-06-23Settings: add GN_SERVER_URLPjotr Prins
2016-06-21logger: add format field (reserve)Pjotr Prins
2016-06-21Logger: switch for logging SQLALCHEMYPjotr Prins
2016-06-21Benchmarking: allow output select with LOG_BENCHPjotr Prins
2016-06-19gn_server: SQL handlingPjotr Prins
2016-06-19Renamed settings so they are grouped togetherPjotr Prins
2016-06-18Logging settingsPjotr Prins
2016-06-18Logger: more infoPjotr Prins
2016-06-18Logger: introducing loggingPjotr Prins
2016-06-18Logging: behavioursPjotr Prins
2016-06-18Logger: improving outputPjotr Prins
2016-06-18Logger: introducing loggingPjotr Prins
2016-06-17ConflictPjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-06-16Introduce behaviour parameters to facilitate developmentPjotr Prins
2016-04-20A few fixes to get the webserver running againPjotr Prins
2016-04-20Show error when GENODIR is missingPjotr Prins
2016-04-20[PATCH 042/100] Sanitizing locationsPjotr Prins
2016-04-20[PATCH 041/100] Fixes for running toolsPjotr Prins
2016-04-20-aPjotr Prins
[PATCH 038/100] Fix compile errors
2016-04-20[PATCH 037/100] WebQtlConfig: sanitizing naming and used varsPjotr Prins
2016-04-20Settled on the _COMMAND syntax over _RUNpjotrp
2016-04-20[PATCH 033/100] Refactored file searchingPjotr Prins
2016-04-20Fine tuning file locatingpjotrp
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
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
2015-06-26Fixed 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.
2015-05-12Add info to warningpjotrp
2015-05-12More elaborate handling of finding pylmmPjotr Prins
2015-05-12Move path search into tools.pypjotrp
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