get_relationship_IsAlignedBy

This relationship connects each alignment to its constituent protein sequences. Each alignment contains many protein sequences, and a single sequence can be in many alignments. Parts of a single protein can occur in multiple places in an alignment. The sequence-id field is used to keep these unique, and is the string that represents the sequence in the alignment and tree text.

Example:

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

id

alignment_method

alignment_parameters

alignment_properties

tree_method

tree_parameters

tree_properties

-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

begin

end

len

sequence_id

properties

-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.