NAME

classify-ali.pl - Classify ALI files based on taxonomic filters

VERSION

version 0.242020

USAGE

classify-ali.pl <indirs> --config=<file> --taxdir=<dir>
    [optional arguments]

REQUIRED ARGUMENTS

<indirs>

Path to input directories containing ALI files [repeatable argument].

--config=<file>

Path to the configuration file specifying the classifier details.

In principle, several configuration file formats are available: XML, JSON, YAML. However, this program was designed with YAML in mind.

The configuration file defines different 'categories'. The order of definition is relevant. Hence, if an ALI matches more than one category, it is classified according to the first one that was defined. Each category has a 'label' that is used to create the corresponding subdirectory for sorting ALI files.

A category is characterized by one or more 'criteria'. To match a category, an ALI must satisfy all criteria. Criteria are thus linked by logical ANDs (and their order of definition is irrelevant).

Each criterion has a 'tax_filter' describing its taxonomic requirements. Wanted taxa are to be prefixed by a + symbol, whereas unwanted taxa are to be prefixed by a - symbol. Wanted taxa are linked by logical ORs while unwanted taxa are linked by logical ANDs. Unwanted taxa should not include wanted taxa because the former ones take precedence over the latter ones. In contrast the opposite helps fine-tuning the tax_filter.

Criteria may also have a 'min_seq_count' and a 'max_seq_count' arguments. These respectively specify the minimum and maximum number of sequences that must pass the tax_filter for the ALI to match the criterion. Minimum defaults to 1, while there is no upper bound by default.

Other conditions are available: 'min_org_count' and 'max_org_count' deal 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 ]

--taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

OPTIONAL ARGUMENTS

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.