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Update help text for clarity: dereplicate --p-mode super #165

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mikerobeson opened this issue Oct 5, 2023 · 0 comments
Open

Update help text for clarity: dereplicate --p-mode super #165

mikerobeson opened this issue Oct 5, 2023 · 0 comments

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@mikerobeson
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mikerobeson commented Oct 5, 2023

This issue was initially discovered by a user in this thread. When a set of sequences, and their associated taxonomy:

  • seq_01 k__Animalia;p__Arthropoda;c__Insecta;o__Hymenoptera;f__;g__;s__
  • seq_02 k__Animalia;p__Arthropoda;c__Insecta;o__Hymenoptera;f__;g__;s__
  • seq_03 k__Animalia;p__Arthropoda;c__Insecta;o__Coleoptera;f__Coccinellidae;g__Harmonia;s__Harmonia axyridis
  • seq_04 k__Animalia;p__Arthropoda;c__Insecta;o__Coleoptera;f__Coccinellidae;g__Harmonia;s__Harmonia axyridis
  • ...

are derepliated using --p-mode super, there is potential for achimeric taxonomy string to be produced:

  • seq_02 k__Animalia;p__Arthropoda;c__Insecta;o__Hymenoptera;f__Coccinellidae;g__Harmonia;s__Harmonia axyridis

This chimeric taxonomy string does not exist in the taxonomy input file.

EDIT: the code is working as intended, as per this post.

EDIT 2: As per EDIT 1, I am changing the focus of this Issue to: clarify the help text for --p-mode super.

@mikerobeson mikerobeson added bug Something isn't working and removed bug Something isn't working labels Oct 5, 2023
@mikerobeson mikerobeson changed the title Potential issue with dereplicate --p-mode super Update help text for clarity: dereplicate --p-mode super Oct 9, 2023
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