get_relationship_IsTaxonomyOf

A genome is assigned to a particular point in the taxonomy tree, but not necessarily to a leaf node. In some cases, the exact species and strain is not available when inserting the genome, so it is placed at the lowest node that probably contains the actual genome.

Example:

get_relationship_IsTaxonomyOf -a < ids > table.with.fields.added

would read in a file of ids and add a column for each field in the relationship.

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the id. If some other column contains the id, use

-c N

where N is the column (from 1) that contains the id.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Command-Line Options

-c Column

This is used only if the column containing id is not the last.

-from field-list

Choose a set of fields from the TaxonomicGrouping entity to return. Field-list is a comma-separated list of strings. The following fields are available:

id

domain

hidden

scientific_name

alias

-rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of strings. The following fields are available:

from_link

to_link

-to field-list

Choose a set of fields from the Genome entity to return. Field-list is a comma-separated list of strings. The following fields are available:

id

pegs

rnas

scientific_name

complete

prokaryotic

dna_size

contigs

domain

genetic_code

gc_content

phenotype

md5

source_id

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added for each requested field. Input lines that cannot be extended are written to stderr.