Before and After 2R #16
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| "jellyfish dump -c -o {output.counts} {input.jf}" | ||
| "jellyfish dump -c -L 2 {input.jf} > {output.counts}" | ||
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| rule extract_features: |
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Since you aren't using this rule, you should just delete it for clarity
| shell: | ||
| "scripts/pca.py --feature-matrices {input.feature_matrices} --groups-fl {params.groups_fl} --plot-fl {output.plot}" | ||
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| rule pca_count_binary: |
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You can add the pca outputs to a list in a top-level rule below. This will allow you to run everything with a single command.
| @@ -32,10 +25,9 @@ merge_batch_size: 512 | |||
| min_doc_freq: 2 | |||
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| # feature extraction | |||
| n_features: 30 | |||
| n_features: 16 | |||
| n_rand_dim: 3000 | |||
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Since we aren't using random projection, you should remove this to avoid confusion
| @@ -32,10 +25,9 @@ merge_batch_size: 512 | |||
| min_doc_freq: 2 | |||
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| # feature extraction | |||
| n_features: 30 | |||
| n_features: 16 | |||
| n_rand_dim: 3000 | |||
| use_binary_features: "--binary" | |||
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Same as above -- with your changes, this isn't used so you should just remove it
| @@ -32,10 +25,9 @@ merge_batch_size: 512 | |||
| min_doc_freq: 2 | |||
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| # feature extraction | |||
| n_features: 30 | |||
| n_features: 16 | |||
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Add a comment to explain that this means 2^16 -- I made this ambiguous by calling it n_features but expecting it to be log2_n_features
| import numpy as np | ||
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| def load_rand_proj(flname): |
| def parse_args(): | ||
| parser = argparse.ArgumentParser() | ||
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| parser.add_argument("--rand-proj-fl", |
| type=str, | ||
| required=True) | ||
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| parser.add_argument("--binary", |
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Remove this -- no longer used
| type=str, | ||
| required=True) | ||
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| parser.add_argument("--passlist-bf", |
These are the updated files that are used to create the plots after count scaling on the 2R chromosome arm.