Matrix#45
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mattheww95
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July 14, 2026 15:29
emarinier
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Looks good to me. Thanks. Just a few comments.
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| lines = [ | ||
| [int(f) if f.isdigit() else f for f in i.split("\t")] | ||
| for i in matrix.read_text().split("\n") | ||
| if i | ||
| ] |
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I understand what this is doing, but it's pretty densely coded. The if i being in-line below the for i ... makes it look like it's supposed to be a classic for-loop, but a tab is missing. Do you know if this is the normal way to format these sorts of code blocks?
| dists_to_matrix, square_matrix, cluster_args.delimiter, matrix_output | ||
| ) | ||
| matrix_task = create_matrix( | ||
| cluster_args, distances, profile_names, output_extension, tg |
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I'd prefer tg as something like task_group, but it's okay.
| >>> beave match -q src/beave/tests/data/R1KC1K.head.tsv -r src/beave/tests/data/R1KC1K.tail.tsv -t 101 -l average -c 8 | ||
| ``` | ||
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| In some instances you may have no need to perform clustering and simply want a distance matrix for other downstream purposes. The matrix option can perform this task and generate a matrix or all pairwise distances in a molten format. e.g. SampleID*1, SampleID_2, dist*{hamming,normalized} |
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Should the * in SampleID*1 and dist*{hamming,normalized} be _, or is this correct?
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Added option to generate distance matrix and exit program.
This may not be needed, holding off on merging for now. May add molten output option.