Update help text for clarity: `dereplicate --p-mode super`
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mikerobeson commented
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
.