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bin/classify-mcl-out.pl  view on Meta::CPAN

with organisms instead of sequences, whereas 'min_copy_mean' and
'max_copy_mean' allow bounding the mean number of gene copies per organism.
All default not no bound.

An example YAML file follows:

    categories:
    - label: strict
      description: strict species sampling
      criteria:
      - tax_filter: [ +Latimeria ]
        min_seq_count: 1
        max_seq_count:
        min_org_count:
        max_org_count:
        min_copy_mean:
        max_copy_mean:
      - tax_filter: [ +Protopterus ]
      # min_seq_count defaults to 1
      # max_seq_count defaults to no upper bound
      # all other also default to no bound
      - tax_filter: [ +Danio, +Oreochromis ]
      - tax_filter: [ +Xenopus ]
      - tax_filter: [ +Anolis, +Gallus, +Meleagris, +Taeniopygia ]
      - tax_filter: [ +Mammalia ]
    - label: loose
      description: loose species sampling
      criteria:
      - tax_filter: [ +Latimeria ]
      - tax_filter: [ +Protopterus ]
      - tax_filter: [ +Danio, +Oreochromis ]
      - tax_filter: [ +Amphibia, +Amniota ]

=for Euclid: file.type: readable

=item --taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.