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gn-uploader: Data uploader for GeneNetwork
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r_qtl2.py
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14 days
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
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
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
2024-02-21
Check that samples/cases are consistent
Frederick Muriuki Muriithi
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
2024-02-20
Stand-alone function to read control file
Frederick Muriuki Muriithi
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
2024-02-05
Do general bundle validation and show errors
Frederick Muriuki Muriithi
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
2024-01-15
Process `na.strings` even for default cases
Frederick Muriuki Muriithi
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
2024-01-09
Raise exception on reading non-existing file
Frederick Muriuki Muriithi
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
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
2024-01-03
Refactor: Extract potentially reusable functions
Frederick Muriuki Muriithi
2024-01-02
Abstract away non-transposed file processing
Frederick Muriuki Muriithi
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
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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