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pylmm was wrong
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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
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Fixes #69
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SQL security fixes
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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.
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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
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Changed order of tabs in statistics panel on trait page
Started working on heatmap
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adding the correlation matrix page
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object for logged in user collections and collections created by
anonymous users.
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scatter plot
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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
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withouot using reaper and caches results so it doesn't need
to read the file every single time someone loads a page
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Created new files for mrna assay tissue data and commonly used
db query related functions
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normalizes the lists of sample values
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Conflicts:
wqflask/base/data_set.py
wqflask/wqflask/views.py
Fixed a couple conflicts to merge Lei's code related to the correlation page
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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
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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
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we might decide to store it differently
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for HLC datasets
Still need to read in file
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and the code seems to run correctly
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Changed "threaded" to True in runserver.py; this fixed issue
related to getting progress bar to work
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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
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operation(s) multiple times
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and gives a report with the percent of total computation time
each takes
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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
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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
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properly, changed SampleList from an object list to object
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values/variances/num_cases are called in DataEditingPage.py
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generated in Jinja2
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