read_sqlite {BoSSA}

Read a pplacer/guppy sqlite file

Description

Read a pplacer/guppy sqlite file

Usage

read_sqlite(sqlite_file,jplace_file=gsub("sqlite$","jplace",sqlite_file),
rank="species")

Arguments

sqlite_file

A pplacer/guppy sqlite path/file name

jplace_file

An optionnal jplace file name. By default, the sqlite file name with the suffix changed from "sqlite" to jplace" is used. If different, the jplace path/name must be specified.

rank

The desired taxonomic assignation rank to extract. default is "species".

Details

As the tree informations are not available in the sqlite file, the jplace file is also required. When the jplace or sqlite files are import into R, the node numbering available in the original file is converted to the class "phylo" numbering.

Value

A list with

runs

The command line used to obtained the sqlite file

taxa

The taxonomic information table

multiclass

The multiclass table

placement_positions

A data frame with the posiotn of each placement in the reference tree

arbre

The tree in class "phylo" over wich placements are performed

edge_key

A matrix with correspondance of node numbering between the original tree in the jplace file and the class phylo tree of the "arbre" component

original_tree

The tree string from the jplace file

For details on the other components (i.e. "placements, "placement_classifications", "placement_evidence", "placement_median_identities", "placement_names", "placement_nbc", "placements", "ranks" and "sqlite_sequence", please, refer to http://erick.matsen.org/pplacer/generated_rst/guppy_classify.html)

Author(s)

pierre lefeuvre

References

http://erick.matsen.org/pplacer/generated_rst/guppy_classify.html

Examples

### the path to the sqlite and jplace files
sqlite_file <- system.file("extdata", "example.sqlite", package = "BoSSA")
jplace_file <- system.file("extdata", "example.jplace", package = "BoSSA")
pplace <- read_sqlite(sqlite_file,jplace_file)