read.nodes.sql

Take an NCBI nodes file and convert it to a data.table

Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.

Scott Sherrill-Mix

taxonomizr

Functions to Work with NCBI Accessions and Taxonomy

read.nodes.sql function

<dl><dt>nodeFile</dt>
<dd>string giving the path to an NCBI node file to read from (both gzipped or uncompressed files are ok)</dd>
<dt>sqlFile</dt>
<dd>a string giving the path where the output SQLite file should be saved</dd>
<dt>overwrite</dt>
<dd>If TRUE, delete nodes table in database if present and regenerate</dd></dl>

Arguments

Read NCBI nodes file — read.nodes.sql

<dl>

<dt>nodeFile</dt>
<dd>string giving the path to an NCBI node file to read from (both gzipped or uncompressed files are ok)</dd>


<dt>sqlFile</dt>
<dd>a string giving the path where the output SQLite file should be saved</dd>


<dt>overwrite</dt>
<dd>If TRUE, delete nodes table in database if present and regenerate</dd>

</dl>

read.nodes.sql: Read NCBI nodes file

Description

Usage

Value

Arguments

References

See Also

Examples