Add ribcounts to sample metadata for dashboard deployment #21
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jeffkaufman
approved these changes
Sep 25, 2023
run.py
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| @@ -264,7 +264,8 @@ def calculate_average_read_length(file_path): | |||
| ribodetector_cmd = [ | |||
| "ribodetector_cpu", | |||
| "--ensure", "rrna", | |||
| "--threads", "24" | |||
| "--threads", "24", | |||
| "--chunk_size", "256" | |||
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nit: in the future it's better practice to put unrelated changes in their own PRs
dashboard/prepare-dashboard-data.py
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| ribocount = int(content) | ||
| sample_metadata[sample]["ribocounts"] = ribocount | ||
| except FileNotFoundError: | ||
| continue |
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I'd like pass here better than continue. If someone later adds code below that's supposed to be within this loop then we wouldn't want to skip it in cases where there was no ribocounts file.
dashboard/prepare-dashboard-data.py
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| try: | ||
| with open(rc_fname, 'r') as file: | ||
| content = file.read().strip() | ||
| ribocount = int(content) |
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nit: I'd write this as int(file.read().strip()); I don't think the intermediate content variable adds anything in this case.
dp-rice
pushed a commit
that referenced
this pull request
Sep 27, 2023
This was referenced Sep 28, 2023
Merged
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Tested my running
prepare-dashboard-data.shwhich successfully completed and saved ribocounts tosample_metadata[sample]["ribocounts"]in cases where the file exists.Also added a
--chunk_sizeargument to the ribocounts function inrun.pyto address memory issues which I suspect were causing the screen processes to die.