Track
Tracks represent annotations associated with the full length of the protein (i.e. per-residue sequence annotations). Tracks are added to proteins using the Protein.add_track() function, or using functions in the shephard.interfaces.si_tracks module.
Tracks must have a track name, as well as either a per-residue symbol annotation or per-residue value annotation, meaning Tracks can be either symbol tracks of value tracks.
Tracks for a given protein can be called using the protein.track(<track name>) function.
Tracks can be removed from proteins using Protein.remove_track() function.
Track Properties
- name()
[Property]: Returns the track name
- values()
[Property]: Returns a list that matches the complete set of values for this track. If no values are assigned returns None
- symbols()
[Property]: Returns a list that matches the complete set of symbols for this track. If no symbols are assigned returns None
- protein()
[Property]: Returns the Protein that this Track is associated with
- track_type()
[Property]: Returns the track type. Will always be one of ‘values’ or ‘symbols’.
Track Functions
- symbol(self, position, safe=True)
Returns a single symbol from the passed position :param position: Starting position of interest. :type position: int :param safe: Flag which if true with throw an exception if a
symbol is requested from a symbol track.
- Returns
Returns a symbol associated with the passed position
- Return type
str
- value(self, position, safe=True)
Returns a single value from the passed position.
- Parameters
position (int) – Starting position of interest.
safe (bool (default = True)) – Flag which if true with throw an exception if a value is requested from a symbol track.
- Returns
Returns a value associated with the passed position
- Return type
float
- symbols_region(self, start, end=None)
Returns a single symbol or a subregion of symbols, depending on if a start and end position are provided or just a start position.
- Parameters
start (int) – Starting position of interest.
end (int) – Ending position of interest.
- Returns
Returns a list of values that maps to the residues in the intervening region defined by start and end).
- Return type
list
- values_region(self, start, end=None)
Returns a single value or a subregion of values, depending on if a start and end position are provided or just a start position
- Parameters
start (int) – Starting position of interest
end (int) – Ending position of interest. If not provided then only the
- Returns
Returns a list of values that maps to the residues in the intervening region defined by start and end)
- Return type
list
Track Attribute Functions
- attributes()
[Property]: Provides a list of the keys associated with every attribute associated with this Track.
- Returns
returns a list of the attribute keys associated with the protein.
- Return type
list
- attribute(self, name, safe=True)
Function that returns a specific attribute as defined by the name.
Recall that attributes are name : value pairs, where the ‘value’ can be anything and is user defined. This function will return the value associated with a given name.
NOTE: Track attributes cannot be loaded or saved to file when Tracks are read/written via interfaces.si_track.
- Parameters
name (str) – The attribute name. A list of valid names can be found by calling the
<Track>.attributes()(which returns a list of the valid names).
- safebool (default = True)
Flag which if true with throw an exception if an attribute with the same name already exists.
- Returns
Will either return whatever was associated with that attribute (which could be anything) or None if that attribute is missing.
- Return type
Unknown
- add_attribute(self, name, val, safe=True)
Function that adds an attribute. Note that if safe is true, this function will raise an exception if the attribute is already present. If safe=False, then an existing value will be overwritten.
NOTE: Track attributes cannot be loaded or saved to file when Tracks are read/written via interfaces.si_track.
- Parameters
name (str) – The parameter name that will be used to identify it
val (<anything>) – An object or primitive we wish to associate with this attribute
safe (bool (default = True)) – Flag which if True with throw an exception if an attribute with the same name already exists, otherwise the newly introduced attribute will overwrite the previous one.
- Returns
- Return type
None - but adds an attribute to the calling object.
- remove_attribute(self, name, safe=True)
Function that removes a given attribute from the Track based on the passed attribute name. If the passed attribute does not exist or is not associate with the Track then this will trigger an exception unless safe=False.
- Parameters
name (str) – The parameter name that will be used to identify it
safe (bool (default = True)) – Flag which if True with throw an exception if an attribute this name does not exists. If set to False then if an attribute is not found it is simply ignored
- Returns
No return type but will remove an attribute from the protein if present.
- Return type
None