Update ponyo simulations #20
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Pull Request Test Coverage Report for Build 394793710
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| """ | ||
| Returns sample ids (found in gene expression df) associated with | ||
| a given list of experiment ids (found in the metadata) | ||
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| Arguments | ||
| ---------- | ||
| experiment_ids_file: str | ||
| File containing all cleaned experiment ids | ||
| metadata_filename: str |
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It might be useful to link to an example of a metadata file here (e.g. the one in human_tests).
ponyo/simulate_expression_data.py
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| @@ -437,20 +469,14 @@ def shift_template_experiment( | |||
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| Arguments | |||
| ---------- | |||
| normalized_data_file: str | |||
| File containing normalized gene expression data | |||
| normalized_data: str | |||
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This should be a pd.DataFrame, right? Not a str?
| @@ -199,12 +199,15 @@ def simulate_by_random_sampling( | |||
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| def simulate_by_latent_transformation( | |||
| num_simulated_experiments, | |||
| normalized_data_file, | |||
| normalized_data_filename, | |||
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One thing you could think about is changing these simulate_by_X functions to also take a DataFrame as input (i.e. normalized_data rather than normalized_data_filename). This would make them consistent with shift_template_experiment, as well as possibly making them faster (although I'm not sure if you're calling these ones in a loop anywhere).
Might be a non-trivial amount of work to update other projects to conform with this, though, so if you want to create a separate issue and think about it later that's fine.
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Good catch! I was waffling about this too. So the other two methods don't run in a for loop so its not required that we use the dataframe. I left them because it makes more sense me to input filenames instead of dataframes (i know its an extra step but feels like its one less hassle) and this one method is more of an exception.
I'll add an issue. One thing I could see doing is making a wrapper function to call the for loop
This PR addresses issues #18 and #17
This PR also updates the test scripts based on these new changes.
Some minor associated updates:
This will be ponyo v 0.3
Note: Linter is failing due to being on a fork