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Enable the check for missing files to act upon a directory where the
R/qtl2 bundle has been extracted into.
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Redesign the InvalidValue error type for the R/qtl2 bundles to list
the errors according to the row and column titles rather than line
numbers. This makes the error-reporting independent on whether or not
the file is transposed.
This will replace the use of the older
`quality_control.errors.InvalidValue` error type that depends on the
line and column numbers, and thus cannot work with transposable files.
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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.
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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.
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Ensure that **ALL** samples/cases/individuals mentioned in any of the
pheno files actually exist in at least one of the geno files.
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R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.
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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.
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Add a function that, given the path to the zip file, will read the
control data. It creates its own context manager.
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Extract the common structure into a separate function and pass in
checkers that return the errors they find.
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Add a function to ensure the values in the geno files are all listed
in the control data under the "genotypes" key.
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* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
`missing_files`
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Add QC a function to list all files listed in the control file, and
another to list only the files missing from the bundle.
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`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 ...
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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.
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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.
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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.
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* 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
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The processing of transposed files is similar across files. This
commit extracts the common parts into a separate function.
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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.
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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.
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