| Age | Commit message (Expand) | Author |
|---|
| 2021-09-23 | Refactor: Move common sample data to separate file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Move common sample test data into a separate file where it can be imported
from, to prevent pylint error R0801 which proved tricky to silence in any
other way.
| Frederick Muriuki Muriithi |
| 2021-09-17 | Fix a number of linting issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Frederick Muriuki Muriithi |
| 2021-09-15 | Fix format of arguments and expected values...* tests/unit/computations/test_heatmap.py: ordering is not longer provided as
a list of tuples; the ordering values are just a list of numbers now. This
commit updates the test to take this into consideration.
* tests/unit/computations/test_qtlreaper.py: the 'Chr' value if numeric, is
represented by an actual number, not a string. This commit updates the code
to take this into consideration.
| Frederick Muriuki Muriithi |
| 2021-09-08 | Ease search for traits and chromosomes...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Return a dict of values rather than list for the traits and chromosomes to
ease searching through the data.
| Muriithi Frederick Muriuki |
| 2021-09-06 | Provide function to organise parsed QTLReaper results...* gn3/computations/qtlreaper.py: Provide a function to organise the results by
trait for easier use down the line.
* tests/unit/computations/test_qtlreaper.py: provide a test to ensure that the
organising function works as expected.
| Muriithi Frederick Muriuki |
| 2021-09-06 | Leave "Chr" value as string when parsing...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The "Chr" value seems to be mostly a name of some sort, despite it being,
seemingly an number. This commit parses the "Chr" value as a string.
It also updates the tests to expec a string, rather than a number for "Chr"
values.
| Muriithi Frederick Muriuki |
| 2021-08-31 | Fix linting errors, minor bugs and reorganise code...* Fix some linting errors and some minor bugs caught by the linter.
Move the `random_string` function to separate module for use in multiple
places in the code.
| Muriithi Frederick Muriuki |
| 2021-08-31 | Parse QTLReaper outputs...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/qtlreaper.py: pass output files
* tests/unit/computations/data/qtlreaper/main_output_sample.txt: sample test
data
* tests/unit/computations/data/qtlreaper/permu_output_sample.txt: sample test
data
* tests/unit/computations/test_qtlreaper.py: add tests
Add code to parse the QTLReaper output data files.
| Muriithi Frederick Muriuki |
