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2015-07-16Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2015-07-15Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2015-07-10Merge /home/lei/genezsloan
2015-07-10Fixed the genofile_parser.py script since some .geno files had been ↵zsloan
incorrectly converted to json Fixed GO search to work with combined searches
2015-07-10Merge https://github.com/genenetwork/genenetwork2Lei Yan
2015-07-10On branch masterLei Yan
2015-07-10Added an OR ("Get Any") search to the index pagezsloan
Fixed several issues with existing searches; for example, the user can type "Chr" before the chromosome parameter (for example LRS=(9 999 Chr2 100 105) )
2015-07-09Added a temporary fix to prevent .geno requiring mapping methods from ↵zsloan
appearing for human groups
2015-07-09Forgot to add one change to the last commitzsloan
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
2015-07-09Some phenotype searches were throwing an error due to an assert statement in ↵zsloan
trait.py. Since I couldn't find the purpose of the assert statement I removed it.
2015-07-07Updated mirror/development sites and changed font color in form control emementszsloan
2015-07-07Also added index column to collectionszsloan
2015-07-07Added index column and changed the way location is displayed for search resultszsloan
2015-07-06Forgot to add the search error page templatezsloan
2015-07-06An error page should be loaded if the user uses a nonexistent search term, ↵zsloan
instead of getting an Internal Server Error
2015-07-02Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2015-07-02Combined searches that didn't work previously should work now, including cis ↵zsloan
and trans combined searches
2015-07-02fix typosArtem Tarasov
2015-07-02fix #80Artem Tarasov
2015-07-02use button for returning to full viewArtem Tarasov
2015-07-01Needed to add a couple parenthesis for transLRS searcheszsloan
2015-07-01Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2015-07-01cis and trans LRS searches now work. Still need to get them working in ↵zsloan
combined searches
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 minor bug where the static loading bar would remain after the mapping ↵zsloan
results were displayed.
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.
2015-06-22Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
Conflicts: wqflask/wqflask/templates/marker_regression.html
2015-06-22Just a few minor changes before pulling Artem's fix to the mapping issue.zsloan
2015-06-22Merge pull request #75 from lomereiter/fix_searchzsloan
fix genotype search
2015-06-22escape docs queryArtem Tarasov
2015-06-22fixed a few potential security issuesArtem Tarasov
2015-06-21fix mapping results loadingArtem Tarasov
2015-06-20fix genotype searchArtem Tarasov
2015-06-18Fixed issue that prevented multiple mapping submissions without refreshing. ↵zsloan
Also changed to where results open in new window instead of colorbox, though an issue remains where the css doesn't seem to be getting imported properly.
2015-06-18removed unused functionArtem Tarasov
2015-06-18fix all_samples_orderedArtem Tarasov
move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-06-18add missing line to webqtlUtilArtem Tarasov
2015-06-17Now you can expand/contract tabs on the trait page by click anywhere on the barzsloan
2015-06-16Finished adding all the extra tools/links below the trait detailszsloan
2015-06-05Added back in some of the options on the trait page; Add, Find, and Verify ↵zsloan
now work. I'll get the other 4 working next.
2015-06-04Fixed a minor issue that was causing position search to not work.zsloan
2015-06-02Wildcards can now be appended to mRNA assay searches, but isn't working ↵zsloan
correctly yet with phenotypes
2015-06-02Added Panduka's Genotation tool link to the trait page, along with the Gene, ↵zsloan
OMIM, and GenBank links
2015-06-02Wildcard search should now work for Genotype searcheszsloan
2015-06-02Wildcard search (*) works for regular mRNA assay and phenotype searches and ↵zsloan
fixed issue with black columns in correlation page
2015-05-26Merge pull request #60 from lomereiter/ppzsloan
add missing file
2015-05-26add missing fileArtem Tarasov
2015-05-26Merge pull request #58 from lomereiter/ppzsloan
Use NVD3 for bar chart and probability plot