getSummaryFile

Retrieval function of the assembly_summary.txt file from NCBI.

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized
way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',
and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database
(Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve
functional annotation for genomic loci. In addition, users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.

Hajk-Georg Drost

biomartr

Genomic Data Retrieval

Haakon Tjeldnes

getSummaryFile function

<dl><dt>db</dt>
<dd>database name. E.g. <code>refseq</code> or <code>genbank</code>.</dd>
<dt>kingdom</dt>
<dd>kingdom for which assembly_summary.txt file shall be
retrieved. See also <code>getKingdoms</code>.</dd>
<dt>file</dt>
<dd>path, local path to total summary file, default is in tmp folder.</dd></dl>

Arguments

Author

Helper function to retrieve the assembly_summary.txt file from NCBI — getSummaryFile

<dl>

<dt>db</dt>
<dd>database name. E.g. <code>refseq</code> or <code>genbank</code>.</dd>


<dt>kingdom</dt>
<dd>kingdom for which assembly_summary.txt file shall be
retrieved. See also <code>getKingdoms</code>.</dd>


<dt>file</dt>
<dd>path, local path to total summary file, default is in tmp folder.</dd>

</dl>

getSummaryFile: Helper function to retrieve the assembly_summary.txt file from NCBI

Description

Usage

Arguments

Author

See Also

Examples