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improve manysketch for (many) metagenome samples #133

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bluegenes opened this issue Sep 26, 2023 · 1 comment
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improve manysketch for (many) metagenome samples #133

bluegenes opened this issue Sep 26, 2023 · 1 comment
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enhancement New feature or request

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@bluegenes
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current manysketch:

  • only allows direct dna or protein sketching, not translation.
  • input csv requires columns: name,genome_filename,protein_filename, which is fantastic for building databases and less fantastic for sketching metagenomes if you want to use both R1/R2 reads without concatenating files.

Note, this mirrors sourmash sketch fromfile template/limitations.

Here, we could try allowing an alternate fromfile input format with columns name,read1,read2 by checking this option if name,genome_filename,protein_filename header is not found or if the user provides some flag. Could we allow translate as a parameter option, too?

@bluegenes bluegenes added the enhancement New feature or request label Sep 26, 2023
@bluegenes
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name,read1,read2 file input was enabled in #184!

...but we don't allow translation yet. will punt to another issue

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