| Age | Commit message (Expand) | Author |
|---|
| 2021-11-04 | Implement `tissue_correlation` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New function (tissue_correlation)
* tests/unit/test_partial_correlations.py ->
tests/unit/computations/test_partial_correlations.py: Move module. Implement
tests for new function
Migrate the `cal_tissue_corr` function embedded in the
`web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in
GN1 and implement tests to ensure it works correctly.
| Frederick Muriuki Muriithi |
| 2021-11-01 | Add test cases for gn3.authentication | BonfaceKilz |
| 2021-10-29 | Feature/biweight reimplementation (#47)...* add biweight reimplementation with pingouin
* delete biweight scripts and tests
* add python-pingouin to guix file
* delete biweight paths
* mypy fix:pingouin mising imports
* pep8 formatting && pylint fixes | Alexander Kabui |
| 2021-10-25 | Implement `partition_all` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: new function (partition_all)
* tests/unit/test_data_helpers.py: tests for function
`gn3.data_helpers.partition_all`
As part of migrating some functions that access the database, this commit
extracts generic processes that can be accomplished on data, and implements
the `partition_all` function, that is equivalent to Clojure's
`partition-all` function.
| Frederick Muriuki Muriithi |
| 2021-10-25 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-10-25 | fix unittests | Alexander Kabui |
| 2021-10-21 | Implement `find_identical_traits` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement function `find_identical_traits`
* tests/unit/test_partial_correlations.py: implement tests for function
`find_identical_traits`
Migrate `web.webqtl.correlation.correlationFunction.findIdenticalTraits`
function in GN1 to here, adding in tests to ensure the migration works in a
bug-compatible version with the original.
| Frederick Muriuki Muriithi |
| 2021-10-21 | Document tests better...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Document the issues better to help with understanding what each test checks
for.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement remaining `fix_samples` functionality...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `dictify_by_samples`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Disable pylint issue...* Disable minor pylint issue.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `control_samples` function as is in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement `control_samples` function
* tests/unit/test_partial_correlations.py: add tests for `control_samples`
function
Implement the function `control_samples` and make it mostly bug-compatible
with the `web/webqtl/correlation/correlationFunction.controlStrain` function
in GN1.
This implementation in GN3 does not do any calls to the database. It will
rely on other functions to provide the data from the database to it.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Migrate `export_informative` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement remaining `fix_samples` functionality...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `dictify_by_samples`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Disable pylint issue...* Disable minor pylint issue.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Implement `control_samples` function as is in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement `control_samples` function
* tests/unit/test_partial_correlations.py: add tests for `control_samples`
function
Implement the function `control_samples` and make it mostly bug-compatible
with the `web/webqtl/correlation/correlationFunction.controlStrain` function
in GN1.
This implementation in GN3 does not do any calls to the database. It will
rely on other functions to provide the data from the database to it.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Migrate `export_informative` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
| Frederick Muriuki Muriithi |
| 2021-09-28 | Retrieve loci names ordered by chromosomes...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps.py: implement function
* tests/unit/test_heatmaps.py: add test
Add a function to retrieve the loci names from the traits, ordered by
chromosomes, in alphabetical order.
This is useful to provide the user with more information on hovering over
the heatmap cells: each cell will now display the locus name, trait name and
value associated with it.
| Frederick Muriuki Muriithi |
| 2021-09-27 | modify unittests | Alexander Kabui |
| 2021-09-27 | add tests for calling wgcna_script | Alexander Kabui |
| 2021-09-27 | fix merge conflicts | Alexander Kabui |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `strain` to `sample`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the terminology used: use `sample` in place of `strain` according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
| Frederick Muriuki Muriithi |
| 2021-09-25 | minor fixes for unittests | Alexander Kabui |
| 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 |
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi |
| 2021-09-22 | add init tests for call to script | Alexander Kabui |
| 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 |
| 2021-09-16 | pylint fixes | Alexander Kabui |
| 2021-09-16 | init tests for wgcna | Alexander Kabui |
| 2021-09-15 | initial test file for wgcna | Alexander Kabui |
| 2021-09-15 | Process data into format usable by heatmaps...* gn3/heatmaps.py: implement `process_traits_data_for_heatmap` function, that
will process the data into a form usable by heatmaps.
* tests/unit/test_heatmaps.py: check that the function processes the data into
the correct form.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Integrate get_lsr_from_chr function...* gn3/heatmaps.py: copy over function
* tests/unit/test_heatmaps.py: add tests
Copy function over from proof of concept and add some tests to ensure it
works as expected.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Reorganise modules...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The heatmap generation does not fall cleanly within the computations or db
modules. This commit moves it to the higher level gn3 module.
| 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 |
| 2021-09-15 | Add missing sample file for tests...* tests/unit/db/data/genotypes/genotype_sample1.geno: new file
Add a missing sample data file needed for unit tests.
| 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 |
| 2021-09-08 | Fix the traits order computations for clustering...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Fix ordering function
* tests/unit/computations/test_heatmap.py: update test
The order of the traits is important for the clustering algorithm, since the
clustering seems to use the distance of one trait from another to determine
how to order them.
This commit also gets rid of the xoffset argument that is not important to
the ordering, and was used in the older GN1 to determine how to draw the
clustering lines.
| 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 |
| 2021-09-01 | Fix linting and typing issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Muriithi Frederick Muriuki |
| 2021-09-01 | Built top-level genotype file parsing function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype files
* tests/unit/db/test_genotypes.py: test parsing is correct
Add the overall genotype files parsing function and tests to check that the
parsing works as expected.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse data lines into markers...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse data lines in file to genetic markers.
* tests/unit/db/test_genotypes.py: test that parsing works.
Add some tests to check that the parsing of the markers works as expected,
and add the code to actually parse the markers.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse the genotype file's data header...* gn3/db/genotypes.py: parse data header
* tests/unit/db/test_genotypes.py: check that header's parse works correctly.
Add tests to check that the parser works as expected. Add code to implement
the parsing and pass the tests.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Implement parsing of genotype labels...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype labels
* tests/unit/db/test_genotypes.py: test that genotype labels are parsed
correctly
As part of parsing the genotype files into usable python data structures,
this commit adds a function to parse the label lines (beginning with "@")
into the appropriate values.
| Muriithi Frederick Muriuki |
