get_entity_ProteinSequence

We use the concept of ProteinSequence as an amino acid string with an associated MD5 value. It is easy to access the set of Features that relate to a ProteinSequence. While function is still associated with Features (and may be for some time), publications are associated with ProteinSequences (and the inferred impact on Features is through the relationship connecting ProteinSequences to Features).

Example:

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

would read in a file of ids and add a column for each filed in the entity.

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.

Related entities

The ProteinSequence entity has the following relationship links:

HasAssertedFunctionFrom Source

IsATopicOf Publication

IsAlignedBy AlignmentTree

IsProjectedOnto ProteinSequence

IsProteinFor Feature

IsProteinMemberOf Family

ProjectsOnto ProteinSequence

Command-Line Options

-c Column

Use the specified column to define the id of the entity to retrieve.

-h

Display a list of the fields available for use.

-fields field-list

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

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.