Non cellranger tags #26
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While cellranger uses the `UB` SAM tag, other scRNA-seq analyses use different SAM tags (*e.g.* `XM`) for the same information. By parameterizing the existing `parse_read` function, this (and other read parsing/filtering options) can be adjusted by the caller without the need for boilerplate code required for a custom callback class. At the same time, by providing the previously hard-coded values as default parameters, compatibility with existing code is kept. All functions using this callback have been extended by optional keyword arguments to allow passing through the newly added parameters. This addresses one out of two issues raised in arogozhnikov#23.
While `BarcodeHandler.__init__` has (optional) parameters to adjust barcode-related options (*e.g.* using non-`CB` SAM tags for the cell barcodes, like `XC`), the static `from_file` function called it without any of those parameters, making it impossible to adjust them when using that function. This is resolved by adding an optional keyword argument dictionary parameters to the static function and passing all argument provided therein, if any, down to the `__init__` call. This addresses one out of two issues raised in arogozhnikov#23.
This was referenced Feb 23, 2024
This is a partial revert of commit f460476 which parameterized the `parse_read` callback and added keyword arguments to all its callers to pass down the arguments like this: ```python count_snps(... , parse_read=parse_read, umi_tag="XM") ``` Howerver, as pointed out by Alex Rogozhnikov, the keyword arguments are not required since a lambda function could be used in their place resulting which even results in more readable code: ```python parse_read_xm = lambda read: parse_read(read, umi_tag="XM") count_snps(... , parse_read=parse_read_xm) ``` Thus, this commit reverts all changes introducing keyword argument to `parse_read` callers, leaving only the parameterization of that callback itself.
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@arogozhnikov: I have rebased this on the updated PR #24. Thus, this now bundles all changes as per your feedback. |
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Cell Ranger uses `CB` SAM tags for the cell barcode and `UB` SAM tags for the UMI but other scRNA-seq pipelines use different tags (*e.g.* `XC` and `XM`). This commit introduces the `CELL_TAG` and `UMI_TAG` environment variables to override the Cell Ranger style defaults. Note: For Demuxalot, this requires upstream changes suggested in the following PR: arogozhnikov/demuxalot#26.
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Interestingly, I did not close this one, github closed it automatically |
That's because this includes #25 and #24 so merging either only this or both of those had the same effect. Thus I added the special 'closes [PR/issue]' directive to my PRs so merging one will automatically close those that become irrelavant by doing so. |
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This is a combination of #24 and #25 in one PR.
Merging this will address all points raised in #23.
closes #23
closes #24
closes #25