get_relationship_ProjectsOnto

This relationship connects two protein sequences for which a clear bidirectional best hit exists in known genomes. The attributes of the relationship describe how good the relationship is between the proteins. The relationship is bidirectional and symmetric, but is only stored in one direction (lower ID to higher ID).

Example:

get_relationship_ProjectsOnto -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 ProteinSequence entity to return. Field-list is a comma-separated list of strings. The following fields are available:

id

sequence

-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

gene_context

percent_identity

score

-to field-list

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

id

sequence

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.