| Age | Commit message (Expand) | Author |
|---|
| 2022-03-22 | Change order of if statements for running genoprob command...Now it checks for pairscan first, just in case interval ends up being
passed (which is an irrelevant parameter for pairscan)
Also added a couple more verbose prints
| zsloan |
| 2022-03-22 | Fixes pylint errors | zsloan |
| 2022-03-22 | Fixed mypy typing errors | zsloan |
| 2022-03-22 | Tried to make the docstrings more consistent | zsloan |
| 2022-03-22 | Add typing to some functions | zsloan |
| 2022-03-22 | Add functions for getting proximal/distal markers for each pseudomarker posit... | zsloan |
| 2022-03-22 | Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't s... | zsloan |
| 2022-03-22 | Added genofile name to inputs for processing R/qtl pair-scan results, since i... | zsloan |
| 2022-03-22 | Removed quotes from beginning and end of chromosome string | zsloan |
| 2022-03-22 | Fixed a cople function calls to use the updated function names | zsloan |
| 2022-03-22 | Create pairscan_for_figure and pairscan_for_table functions that return the D... | zsloan |
| 2022-03-22 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ... | zsloan |
| 2022-03-22 | Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ... | zsloan |
| 2022-03-22 | Added pairscan boolean kwarg and process_rqtl_pairscan function for reading i... | zsloan |
| 2022-03-22 | Added line priting pair-scan results to CSV and changed the default step-size... | zsloan |
| 2022-03-22 | - Added scan_func function that determines whether scanone or scantwo...(pairscan) is used
- For pairscan default to using step 20 (subject to change, but some
step is required during calc.genoprob to make it run fast enough)
- Added some new verbose prints
| zsloan |
| 2022-03-22 | Added option for running pairscan to rqtl_wrapper.R | zsloan |
| 2022-03-18 | README: Update CI badge subdomain....The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org.
* README.md: Update CI badge subdomain.
| Arun Isaac |
| 2022-03-18 | Clean all csv fields before diffing...There was a subtle bug where "csvdiff" generated an error related to
"different column headings" caused something akin to diffing: "a, b \n, ..."
with "a, b\n, ...".
* gn3/csvcmp.py (csv_diff): Clean csv texts before any diffing.
* tests/unit/test_csvcmp.py (test_csv_diff_same_columns): Modify test case to
capture aforementioned bug.
| BonfaceKilz |
| 2022-03-18 | Create new function for cleaning individual fields in csv text...* gn3/csvcmp.py (clean_csv_text): New function.
* tests/unit/test_csvcmp.py: Import "csv_text".
(test_clean_csv_text): Test case for the above.
| BonfaceKilz |
| 2022-03-15 | Feature/refactored pca (#79)...* compute zscore function
* test case for computing zscore
* function to compute pca
* generate scree plot data
* generate new pca trait data from zscores and eigen_vec
* remove redundant functions
* generate factor loading table data
* generate pca temp dataset dict
* variable naming and error fixes
* unit test for processing factor loadings
* minor fixes for generating temp pca dataset
* pass datetime as argument to generate_pca temp dataset function
* add unittest for caching pca datasets
* cache temp datasets
* ignore missing imports for sklearn
* mypy fixes
* pylint fixes
* refactor tests for pca
* remove ununsed imports
* fix for generating pca traits vals
* mypy and code refactoring
* pep8 formatting and add docstrings
* remove comments /pep8 formatting
* sort eigen vectors based on eigen values
* minor fix for zscores
* fix for rounding variance ratios
* refactor tests
* rename module to pca
* rename datasets to traits
* fix failing tests
* fix caching function
* fixes return x and y coordinates for scree plot
* expand exception scope
* fix for deprecated numpy.matrix function
* fix for failing tests
* pep8 fixes
* remove comments
* fix merge conflict
* pylint fixes
* rename module name to test_pca | Alexander Kabui |
| 2022-03-14 | Dummy White Space commit to fix laminar | BonfaceKilz |
| 2022-03-14 | Sort import lines | BonfaceKilz |
| 2022-03-14 | Only loop through the diff's modifications if it exists | BonfaceKilz |
| 2022-03-14 | Given a csv text and permissible headers, extract invalid headers...* gn3/csvcmp.py (extract_invalid_csv_headers): New function.
* tests/unit/test_csvcmp.py: Import "extract_invalid_csv_headers".
(test_extract_invalid_csv_headers_with_some_wrong_headers): Test case for the
above.
| BonfaceKilz |
| 2022-03-14 | Get all permissible column data...* gn3/csvcmp.py: Import "Any" and "List".
(get_allowable_sampledata_headers): New function.
* tests/unit/test_csvcmp: Import "get_allowable_sampledata_headers".
(test_get_allowable_csv_headers): Test case for the above.
| BonfaceKilz |
| 2022-03-12 | Fix pylint errors in unit_tests | BonfaceKilz |
| 2022-03-12 | Remove unused imports | BonfaceKilz |
| 2022-03-12 | Fix mypy issues | BonfaceKilz |
| 2022-03-12 | Fix pylint issues | BonfaceKilz |
| 2022-03-12 | README: Replace "unit-test" instructions with "pytest" | BonfaceKilz |
| 2022-03-12 | Compose csv-diff command within single quotes...* gn3/csvcmp.py (csv_diff): Use single quotes. There was a change in 6d39c92
that broke this.
| BonfaceKilz |
| 2022-03-12 | Delete noisy "print" statement | BonfaceKilz |
| 2022-03-12 | Store the first element as strain_id | BonfaceKilz |
| 2022-03-12 | Append the strain name when extracting "actions"...* gn3/db/sample_data.py (__extract_actions): During updates, make sure that
the strain name is part of the returned string when extracting "actions".
* tests/unit/db/test_sample_data.py: Add test cases for the above.
| BonfaceKilz |
| 2022-03-12 | Apply auto-pep8 to sample_data.py and it's test file | BonfaceKilz |
| 2022-03-12 | Add missing return type-annotations...* tests/unit/db/test_sample_data.py (delete_sample_data): Add missing return
type for type annotations.
(insert_sample_data): Ditto.
| BonfaceKilz |
| 2022-03-12 | Update how data is updated by re-using existing functions...* gn3/db/sample_data.py (get_sample_data_ids): Re-use "delete_sample_data" and
"insert_sample_data" when updating data; and also add logic for updating
modified data.
* tests/unit/db/test_sample_data.py: Add tests for the above.
| BonfaceKilz |
| 2022-03-12 | Create action dict that's created when updating data...* gn3/db/sample_data.py (__extract_actions): An update on a vector of data can
contain: inserts, deletes and updates. This functions extracts these actions
during an update.
* tests/unit/db/test_sample_data.py (test_extract_actions): Add test-case for
the above.
| BonfaceKilz |
| 2022-03-12 | Add test cases for inserting and deleting data...* tests/unit/db/test_sample_data.py (test_insert_sample_data): Test inserting
data.
(test_delete_sample_data): Test deleting data.
| BonfaceKilz |
| 2022-03-12 | Remove check for inserted data when inserting individual data...* gn3/db/sample_data.py (insert_sample_data)[__insert_data]: Move check to the
main body. With this check here, you have 3 redundant checks. For a successful
insert, it will insert the first value to the `PublishData` table and ignore the
rest of the inserts.
| BonfaceKilz |
| 2022-03-12 | Make `_map` a constant...* gn3/db/sample_data.py: Now constant, `_MAP`.
(delete_sample_data)[__delete_data]: Replace `_map` with `_MAP`.
(insert_sample_data)[__insert_data]: Ditto.
| BonfaceKilz |
| 2022-03-12 | Fix faulty SQL query string when deleting case-attributes | BonfaceKilz |
| 2022-03-12 | Explicitly get CaseAttributeId and fix broken sql query...* gn3/db/sample_data.py (insert_sample_data): Use correct query string. Also,
use CaseAttributeId to determine whether case-attributes were inserted. If so,
do not attempt an insert.
| BonfaceKilz |
| 2022-03-12 | Remove duplicate params...* gn3/db/sample_data.py (insert_sample_data)[__insert_case_attribute]: Remove
extra parameters.
| BonfaceKilz |
| 2022-03-12 | Remove dead code | BonfaceKilz |
| 2022-03-12 | Check whether publish data already exists before inserting...* gn3/db/sample_data.py (insert_sample_data): If data already exists in the
table, do not attempt an insert; otherwise, an error will be generated.
| BonfaceKilz |
| 2022-03-12 | Fill in empty values in csv text with: "x"...* gn3/csvcmp.py (fill_csv): Update this function to allow empty lists to be
filled with the default value(set in the args).
* tests/unit/test_csvcmp.py (test_fill_csv): Update test to capture above.
| BonfaceKilz |
| 2022-03-12 | Remove test cases related to sample data...Most of this functions were moved to their own module.
| BonfaceKilz |
| 2022-03-12 | Fetch id's separately for the insertion edge-case...* gn3/db/sample_data (get_sample_data_ids): Add an extra condition that caters
for inserts: during inserts, joins won't work when fetching the strain_id,
publishdata_id, and strain_name. In this case, just create 2 separate queries
to do that work.
| BonfaceKilz |
