Extractor functions for ConTax data

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Description

Extracting taxonomic information from ConTax data sets.

Usage

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getDomain(header)
getPhylum(header)
getClass(header)
getOrder(header)
getFamily(header)
getGenus(header)
getTag(header)
getTaxonomy(header)

Arguments

header

A vector of texts, typically the Header from a Fasta object, containing taxonomy information in the proper format.

Details

The ConTax data sets are Fasta objects, where the Header line follows a strict format.

The Header always starts with a short text, a Tag, which is a unique identifier for every sequence. The function getTag will extract this from the header.

After the Tag follows one or more tokens. One of these tokens must be a string with the following format:

"k__<...>;p__<...>;c__<...>;o__<...>;f__<...>;g__<...>;"

where <...> is some proper text. Here is an example of a proper string:

"k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;"

The functions getDomain, ..., getGenus extract the corresponding information from the header. getTaxonomy combines all taxonomy extractors, combines these in a data.frame and imputes missing taxa with parent taxa.

Value

A vector containing the sub-texts extracted from each header text.

Author(s)

Lars Snipen.

See Also

contax.trim, medoids.

Examples

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