feat(cram): slice local files #11
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… type (e.g., calls slice_cram when slicing genomic data
Updating 'slice' branch with 'main'.
…ust needs the data_type and data_path logic to be added in
cmdoret
requested changes
Feb 9, 2024
modo/cram.py
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| def slice_array(): # to be defined after we get more knowledge of how the | ||
| return None # data looks like |
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| def slice_array(): # to be defined after we get more knowledge of how the | |
| return None # data looks like | |
| def slice_array(): | |
| raise NotImplementedError("Slicing of arrays not supported yet") |
suggestion: explicit error message.
modo/cram.py
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| Examples | ||
| -------- | ||
| >>> slice("data/ex1/demo1.cram", "chr1:100-200") | ||
| def slice(data_name: str, data_path: str, coords: str): |
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suggestion: passing a DataEntity here would reduce the number of arguments needed. All the information we need (path, name, ...) is encapsulated in the object.
modo/cram.py
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| ... | ||
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| # split up coordinate string "chr:start-end" into its three elements | ||
| coords = coords.replace("-", ":") |
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fix: this is dangerous, as it is possible for a chromosome name to contain -. This would break in such cases (chr1-human:1-100 -> chr1:human:1:100 -> 4 parts).
modo/cram.py
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| Usage: | ||
| ----- | ||
| >>> x = slice("data/ex1/demo1.cram", "chr1:100-200") | ||
| >>> for read in x: | ||
| print(read) |
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| Usage: | |
| ----- | |
| >>> x = slice("data/ex1/demo1.cram", "chr1:100-200") | |
| >>> for read in x: | |
| print(read) |
docs: this usage describes the slice function.
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This is left over from before the split into slice() and slice_cram(), and I forgot to change this to slice_cram()
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I have added a slice() and a slice_cram() functions.
MODO.slice(data: str, coords: str) will call slice(), which in turn will call the right slicing function depending on the data format/type that is being sliced (e.g., if it is a CRAM file, it will call slice_cram())
The two things missing ... please add them in ... are,
(1) determining the data_type (CRAM/array/etc.) of the data, so the right slicing function can be called.
(2) determining the data_path, so the slicing function will know where the data is, and whether it is a local file or on a server (logic for this will be added in later, currently it deals with local files).