| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-12-09 | Handle common typo likely to exist in control files. | Frederick Muriuki Muriithi | |
| 2024-10-24 | Fix linting and typing errors. | Frederick Muriuki Muriithi | |
| 2024-10-21 | Add utilities for reading text files and csv files | Frederick Muriuki Muriithi | |
| The function `read_text_file(…)` will read the raw text file and return the content line by line. The function `read_csv_file(…)` builds on `read_text_file(…)` to read a file as a character-separated-values file. The field separator, and comment_char characters can be provided to customise how the CSV file is read. | |||
| 2024-10-17 | Ignore comment lines. | Frederick Muriuki Muriithi | |
| 2024-10-14 | Improve error messages for R/qtl2 code. | Frederick Muriuki Muriithi | |
| 2024-08-12 | Bug: Ensure file type values are lists. | Frederick Muriuki Muriithi | |
| 2024-08-12 | Add utility to transpose CSVs, renaming the original file. | Frederick Muriuki Muriithi | |
| 2024-08-12 | Rename module: Module contains exceptions classes. | Frederick Muriuki Muriithi | |
| 2024-08-09 | Read R/qtl2 control data from a directory with extracted files. | Frederick Muriuki Muriithi | |
| 2024-08-08 | Function to transpose CSV files. | Frederick Muriuki Muriithi | |
| Some files come in a transposed form, so we need to transpose them again in order to use the same processing code for all files. | |||
| 2024-08-08 | Add utility function to extract R/qtl2 zip bundles | Frederick Muriuki Muriithi | |
| 2024-06-20 | Check for special files that might share names/extensions | Frederick Muriuki Muriithi | |
| Check for special files and hidden files that might be inadvertently added to the zip bundle by the operating system in use that might share names and/or extensions with the main bundle files. | |||
| 2024-02-21 | Check that samples/cases are consistent | Frederick Muriuki Muriithi | |
| Ensure that **ALL** samples/cases/individuals mentioned in any of the pheno files actually exist in at least one of the geno files. | |||
| 2024-02-20 | Generalise fetching of samples/cases/individuals. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Read samples from geno file. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Read each file separately | Frederick Muriuki Muriithi | |
| Provide the function 'read_file_data' in the 'r_qtl.r_qtl2' module to read each file in the bundle separately. The function 'file_data' in the 'r_qtl.r_qtl2' module reads *ALL* the files of a particular type (e.g. geno files) and returns a single generator object with the data from *ALL* the files. This does not render itself very useful for error checking. We needed a way to check for errors, and report them for each and every file in the bundle, for easier tracking and fixing. | |||
| 2024-02-20 | Stand-alone function to read control file | Frederick Muriuki Muriithi | |
| Add a function that, given the path to the zip file, will read the control data. It creates its own context manager. | |||
| 2024-02-16 | Replace genotype codes with values in control file. | Frederick Muriuki Muriithi | |
| 2024-02-16 | Convert missing value codes to None | Frederick Muriuki Muriithi | |
| 2024-02-16 | Strip comment lines. | Frederick Muriuki Muriithi | |
| 2024-02-16 | Read raw text data from a file in the zip bundle | Frederick Muriuki Muriithi | |
| 2024-02-13 | Make "FILE_TYPES" part of public interface for module/package. | Frederick Muriuki Muriithi | |
| 2024-02-05 | Check that data in geno file is valid | Frederick Muriuki Muriithi | |
| Add a function to ensure the values in the geno files are all listed in the control data under the "genotypes" key. | |||
| 2024-02-05 | Do general bundle validation and show errors | Frederick Muriuki Muriithi | |
| * Display any and all errors on the UI * Move `validate_bundle` to QC module and refactor to use `missing_files` | |||
| 2024-02-02 | List file types in a single place for easier reuse | Frederick Muriuki Muriithi | |
| 2024-02-02 | Ensure control file defaults are set up in code. | Frederick Muriuki Muriithi | |
| 2024-01-16 | Provide defaults for various control variables | Frederick Muriuki Muriithi | |
| `na.strings` has a default value of "NA" as stated in https://kbroman.org/qtl2/assets/vignettes/input_files.html#CSV_files quote: > Missing value codes will be specified in the control file (as > na.strings, with default value "NA") and will apply across all > files, so a missing value code for one file cannot be an allowed > value in another file. for `comment.char` > The CSV files can include a header with a set of comment lines > initiated by a value specified in the control file as comment.char > (with default value "#"). for `sep`: The default separator is expected to be the comma, as stated in https://kbroman.org/qtl2/assets/vignettes/input_files.html#field-separator quote: > If the data files use a separator other than a comma ... | |||
| 2024-01-15 | Process `na.strings` even for default cases | Frederick Muriuki Muriithi | |
| There was a bug where the `na.strings` were not processed correctly if the user called the `r_qtl.r_qtl2.file_data(...)` function without explicitly providing the `process_*` arguments. This commit fixes that. | |||
| 2024-01-15 | Extract common functional tools to separate package. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Provide convenience functions to avoid subtle call errors | Frederick Muriuki Muriithi | |
| 2024-01-10 | Make identifier column name explicit | Frederick Muriuki Muriithi | |
| Since the R/qtl2 bundle generator could name the identifier column anything, this commit converts the incoming identifier column name into something explicit that we know and can use. | |||
| 2024-01-09 | Raise exception on reading non-existing file | Frederick Muriuki Muriithi | |
| The validation checks ensure that whatever files are listed in the control file exist in the zip file bundle. It is still possible, however, that the code tries to read a file that does not exist in the file and is not listed in the control file. In those cases, raise the appropriate exception. | |||
| 2024-01-08 | Upload R/qtl2 zip bundle and check for errors. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Parse sex information from R/qtl bundle. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Parse cross information from R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Process sex and cross information data in "covar" files. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Parse multiple files with same file key. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Use generic parser. Remove obsoleted functions. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Parse founder_geno files. Generalise parsing files. | Frederick Muriuki Muriithi | |
| * Add tests for parsing "founder_geno" files * Extract common file parsing structure out to more general function * Use generic function to parse "founder_geno" file in test | |||
| 2024-01-03 | Parse the phenotype data from the R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Rename argument and add documentation to functions. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Extract processing of transposed files into reusable function. | Frederick Muriuki Muriithi | |
| The processing of transposed files is similar across files. This commit extracts the common parts into a separate function. | |||
| 2024-01-03 | Refactor: Extract potentially reusable functions | Frederick Muriuki Muriithi | |
| The processing of transposed files is probably going to be very similar, thus the need to extract some reusable code from the geno-file-specific function in preparation. | |||
| 2024-01-02 | Abstract away non-transposed file processing | Frederick Muriuki Muriithi | |
| Since the processing of non-transposed files is mostly similar, abstract away the common operations into a separate function and use the function instead of repeating the same pattern of code throughout the codebase. | |||
| 2024-01-02 | Cleanup: Fix linting and typing errors and update docs. | Frederick Muriuki Muriithi | |
| 2023-12-28 | Rework parsing of transposed geno files. | Frederick Muriuki Muriithi | |
| 2023-12-28 | Handle transposed geno files. | Frederick Muriuki Muriithi | |
| 2023-12-27 | Tests: Test parsing of non-transposed geno files. | Frederick Muriuki Muriithi | |
| Check that the parsing of non-transposed geno files. Leave in failing test for transposed geno files. | |||
| 2023-12-27 | Tests: Add tests for parsing gmap files. | Frederick Muriuki Muriithi | |
| 2023-12-25 | Generalise to read both genetic and physical maps. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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