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2021-09-16add function to compose and run wgcna scriptAlexander Kabui
2021-09-16function to parse form data and write to json fileAlexander Kabui
2021-09-15initial test file for wgcnaAlexander Kabui
2021-09-15init wgcna file to run r script and preprocess dataAlexander Kabui
2021-09-15remove golang package causing build failureAlexander Kabui
2021-09-15Update entry-point function for heatmap generationFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Copy over code from the proof-of-concept implementation and clean it up a little for the entry-point function for heatmap generation via the API
2021-09-15Generate heatmaps in a single plotFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add a function to generate the heatmaps for each chromosome into a single plot.
2021-09-15Process data into format usable by heatmapsFrederick Muriuki Muriithi
* 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.
2021-09-15Integrate get_lsr_from_chr functionFrederick Muriuki Muriithi
* 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.
2021-09-15Reorganise modulesFrederick Muriuki Muriithi
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.
2021-09-15Fix format of arguments and expected valuesFrederick Muriuki Muriithi
* 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.
2021-09-15Add missing sample file for testsFrederick Muriuki Muriithi
* tests/unit/db/data/genotypes/genotype_sample1.geno: new file Add a missing sample data file needed for unit tests.
2021-09-15minor fixesAlexander Kabui
2021-09-15rename variables && delete debugsAlexander Kabui
2021-09-15Fetch IMAGE_DIR env and add img locationAlexander Kabui
2021-09-14remove debug statementsAlexander Kabui
2021-09-14function to generate rand str for imageAlexander Kabui
2021-09-14plot plotDendroAndColors and generate pngAlexander Kabui
2021-09-14construct gene co-expression network & module detectionAlexander Kabui
2021-09-14compute the softthreshholdAlexander Kabui
2021-09-14Checking data for excessive missing valuesAlexander Kabui
2021-09-14load the required data for analysisAlexander Kabui
2021-09-14init commit for wgcna scriptAlexander Kabui
2021-09-09Update proof-of-concept codeMuriithi Frederick Muriuki
* Add individual heatmaps * Add dendograms * Merge multiple heatmaps to single plot Updated the proof of concept code to provide a sample of what is needed to generate the appropriate heatmaps. To generate the sample heatmaps, one can run something like: env SQL_URI="mysql://webqtlout:webqtlout@127.0.0.1:3306/db_webqtl" \ python3 qtlfilesexport.py assuming that the database can be accessed at 127.0.0.1:3306
2021-09-08Ease search for traits and chromosomesMuriithi Frederick Muriuki
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.
2021-09-08Parse Chr value as int where possibleMuriithi Frederick Muriuki
* To ease sorting of data by numerical order down the line, sort the "Chr" values by numerical order.
2021-09-08Remove extraneous text to ease sortingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Change the id from 'T<n>' to simply '<n>' to ease sorting of the trait results by numerical order rather than string order.
2021-09-08Fix the traits order computations for clusteringMuriithi Frederick Muriuki
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.
2021-09-06Provide function to organise parsed QTLReaper resultsMuriithi Frederick Muriuki
* 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.
2021-09-06Leave "Chr" value as string when parsingMuriithi Frederick Muriuki
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.
2021-09-06Handle type-coercion exceptionsMuriithi Frederick Muriuki
* gn3/computations/qtlreaper.py: handle exceptions Sometimes, the values being parsed are plain strings and cannot be cast to the float types. This commit handles that by casting only those values that can be cast to float, and returning the others as strings.
2021-09-06Find nearest markerMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Migrate the `web.webqtl.heatmap.Heatmap.getNearestMarker` function in GN1 to GN3.
2021-09-01Fix linting and typing issuesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-09-01Built top-level genotype file parsing functionMuriithi Frederick Muriuki
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.
2021-09-01Parse data lines into markersMuriithi Frederick Muriuki
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.
2021-09-01Parse the genotype file's data headerMuriithi Frederick Muriuki
* 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.
2021-09-01Implement parsing of genotype labelsMuriithi Frederick Muriuki
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.
2021-08-31Fix linting errors, minor bugs and reorganise codeMuriithi Frederick Muriuki
* 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.
2021-08-31Update `heatmap_data` function: remove extraneous dataMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: update function * gn3/db/traits.py: new function Remove extraneous data and arguments from the function. - Load the genotype file - Generate traits file - Provide both raw traits data, and exported traits data in return
2021-08-31Fix testMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The number of the arguments to the function changed, and so the tests for the function needed to be updated.
2021-08-31Parse QTLReaper outputsMuriithi Frederick Muriuki
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.
2021-08-31Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_generation
2021-08-31Fix bugs with `run_reaper` functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/qtlreaper.py: Fix some bugs * qtlfilesexport.py: Test out running rust-qtlreaper Test out the qtlreaper interface code and fix some bugs caught in the process.
2021-08-31Provide utilities for genotype filesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: New module * gn3/settings.py: Add new configuration variable * qtlfilesexport.py: Test out new code Add a module containing functions dealing with the genotype files. Add a configuration variable to point to the location of the genotype files.
2021-08-30Update documentation on genotype filesMuriithi Frederick Muriuki
* Provide documentation on downloading and using the genotype files.
2021-08-30Fix issues with traits file formatMuriithi Frederick Muriuki
* README.md: update header: Traits ==> Trait * gn3/computations/qtlreaper.py: update header: Traits ==> Trait * qtlfilesexport.py: Choose only BXD strains Rename the first column header from "Traits" to "Trait" to correspond with what `rust-qtlreaper` expects. Choose only the BXD strains for the proof-of-concept example - this helped bring out the fact that the traits file SHOULD NOT contain a strain column for a strain that does not exist in the genotype file in consideration. If the traits file has a strain column which does not exist in the genotype file, then `rust-qtlreaper` fails with a panic, since, from what I can tell, it tries to get a value from the genotype file for the non-existent strain, which results to a `None` type. Subsequent attempts at running an operation on the `None` type lead to the panic.
2021-08-30Remove empty lineMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Remove empty line at the end of the traits file
2021-08-30Fix some linting errors and minor bugs.Muriithi Frederick Muriuki
2021-08-30Implement module for interfacing with rust-qtlreaperMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: move `generate_traits_file` function to new module * gn3/computations/qtlreaper.py: new module to interface with the `rust-qtlreaper` utility. * gn3/settings.py: Provide setting for the path to the `rust-qtlreaper` utility * qtlfilesexport.py: Move `random_string` function to new module. Update to use functions in new module. Provide a module with functions to be used to interface with `rust-qtlreaper`. This module essentially contains all the functions that are needed to build the files needed for, and to run the qtlreaper utility.
2021-08-30Document acquired knowledge on `rust-qtlreaper`Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps/heatmaps.py: document format of the traits file To assist future developers, and development of the system, this commit documents some of the hard-won knowledge about the operation of the system to ease future development of the system. The documentation, if good, might also help with future onboarding of new developers to the system.
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