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2013-01-10Edited marker_regression.coffee to make every sub-manhattan plotZachary Sloan
for each chromosome display Created css file for the marker_regression page Currently has display issue where the permutation histogram is overlapping with the manhattan plot
2013-01-10Made Chromosome class in marker_regression.coffee; currentZachary Sloan
it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that.
2013-01-10Made x-axis values into ints; committing before trying to add multiple graphsZachary Sloan
for each chromosome
2013-01-10Worked with the manhattan plot coffeescript to set x-axis and changeZachary Sloan
the plot point sizes and remove lines
2013-01-09Manhattan plot results are appearing correctly for chromosome 1Zachary Sloan
2013-01-09The histogram coffeescript is now in its own class and the graphZachary Sloan
still displays correctly
2013-01-09Checking in before putting the histogram coffeescript into its ownZachary Sloan
class
2013-01-09More or less finished the permutation histogramZachary Sloan
2013-01-09Got the permutation plot working as a line plot; still need to makeZachary Sloan
it into a bar graph, though
2013-01-09jqplot addedZachary Sloan
2013-01-09Got the marker regression page to display againZachary Sloan
Passed lrs_array values as js_data for the permutation histogram
2013-01-08js_data is being printed out (seemingly) correctly now for theZachary Sloan
marker_regression page
2013-01-08Created IndChromosome class in species.py and wrote functions forZachary Sloan
chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugsZachary Sloan
Added a couple utility functions to the Chromosomes class in species.py
2013-01-04Continued rewriting marker_regression.py codeZachary Sloan
2013-01-04Correct results are being returned from reaper for the marker regression pageZachary Sloan
2013-01-03Began working on marker_regression.py and created Chromosomes classZachary Sloan
in species.py
2013-01-03marker_regression page is up againZachary Sloan
2013-01-03Created template for marek regression page and made the compute button directZachary Sloan
to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-20Changed layout of marker regression optionsZachary Sloan
2012-12-20The control locus field in the interval mapping settings is now disabled ifZachary Sloan
"choose closest control" is set to "yes"
2012-12-20Made composite mapping options show/hide for the interval mapping sectionZachary Sloan
2012-12-20More changes to the layout of interval mapping optionsZachary Sloan
2012-12-20Continued to customize the interval mapping menuZachary Sloan
2012-12-20Improved appearance/layout of the interval mapping tab using bootstrapZachary Sloan
2012-12-20Form data passed via POST for marker regressionZachary Sloan
Removed "Use Parents" and "Use Weighted" Created text box to input # permutations for pair scan
2012-12-18Changed html for the marker regression tabZachary Sloan
Created file show_trait_mapping_tools.coffee to handle submitting the form to the marker regression page Changed form name/id in show_trait.html to "trait_data_form"
2012-12-18Created new file species.py and species class object TheSpeciesZachary Sloan
Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests
2012-12-07Got links working for statistics table labelsZachary Sloan
2012-12-07Got basic statistics in show_trait to display the correct numberZachary Sloan
of samples for each group Got show_trait page to display for genotype traits
2012-12-07Got show_trait page to appear again for phenotype traitsZachary Sloan
Need to see why other samples list doesn't appear for traits in BXDPublishedPhenotypes
2012-12-06All 10 stats workingZachary Sloan
2012-12-06Continued work on basic statistics table in show_traitZachary Sloan
Continued work towards getting show_trait to work with phenotype traits
2012-12-06Added minimum/maximum to basic statistics tableZachary Sloan
Continued bug-shooting related to getting show_trait running with phenotype traits
2012-12-06Got show_trait running again for MrnaAssay traitsZachary Sloan
2012-12-06Made many small changes to show_trait/data_set/search_results/trait toZachary Sloan
remove use of the formData object and cursor
2012-12-05Renamed webqtlTrait.py to trait.pyZachary Sloan
Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough)
2012-12-05Continued to make changes related to getting rid of cursor/db_connZachary Sloan
and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again
2012-12-04Changed parser to allow quotes (i.e. name="rw williams")Zachary Sloan
Renamed webqtlTrait to GeneralTrait and began rewriting parts Changed database code in many places to use simple sqlalchemy
2012-12-04Began changing references to cursor/db_conn to use sqlalchemyZachary Sloan
Wrote function for phenotype author searches
2012-11-30Added example of escaping strings now that trasitioning to simple SQLAlchemyZachary Sloan
2012-11-30Started switching to using basic sqlalchemy to handle db connection/queriesZachary Sloan
Began fixing bugs related to this fix, still in progress
2012-11-30Finished pValue searchZachary Sloan
Got headers working in search page
2012-11-30Got searches working for RANGE and MEAN commandsZachary Sloan
Created a file where renamed variables will be listed for future reference
2012-11-29Changed a number of variables (riset to group, db to dataset)Zachary Sloan
Put most of the code for cisLRS and transLRS searches into the class CisTransLrsSearch (might change this name to something else later) Simplified escape code for searches in do_search.py Got search_results working again after some changes
2012-11-29Got LRS searches working with 5 parametersZachary Sloan
2012-11-28Got cisLRS search working (in web service) for searches with > or < (ex. LRS>99)Zachary Sloan
search_term is always a list now ([99] in the example LRS>99)
2012-11-28Changed parser to split by ">=" and "<="Zachary Sloan
2012-11-28Changed parser.py to deal with the wild card character (*) and to split byZachary Sloan
">" and "<" in addition to "=" and ":"
2012-11-28Made some small changes to get code working for genotype searchesZachary Sloan
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