goatools.godag.relationship_str module

Create strings representing relationships on GO Terms.

For example:

                   +------- has 'part_of' relationship(s)
                   |    +-- pointed to by a GO ID with a 'part_of' relationship
                   |    |
                   V    V
GO:0008150 L00 D00 .... .rdu biological_process
GO:0050896 L01 D01 .... .rdu response to stimulus
GO:0042221 L02 D02 .... p... response to chemical
GO:0032501 L01 D01 .... .rdu multicellular organismal process
GO:0003008 L02 D02 .... .r.. system process
GO:0051606 L02 D02 .... .... detection of stimulus
GO:0050877 L03 D03 .... .rdu nervous system process
GO:0009593 L03 D03 P... .... detection of chemical stimulus
GO:0007600 L04 D04 .... pr.. sensory perception
GO:0050906 L03 D03 P... .... detection of stimulus involved in sensory perception
GO:0050890 L04 D04 .... .... cognition
GO:0050907 L04 D04 P... .... detection of chemical stimulus involved in sensory perception
GO:0007606 L05 D05 .... p... sensory perception of chemical stimulus
GO:0050893 L05 D05 P... .... sensory processing
GO:0050911 L05 D05 P... .... detection of chemical stimulus involved in sensory perception of smell
GO:0007608 L06 D06 .... p... sensory perception of smell

class goatools.godag.relationship_str.RelationshipStr(relationships=None)

Bases: object

Create strings representing relationships on GO Terms.

rel2chr = {'negatively_regulates': 'D', 'part_of': 'P', 'positively_regulates': 'U', 'regulates': 'R'}

rev2chr = {'negatively_regulates': 'd', 'part_of': 'p', 'positively_regulates': 'u', 'regulates': 'r'}

str_relationships(goobj)

Get a string representing the presence of absence of relationships. Ex: P…

str_rel_short(goobj)

Get a string representing the presence of absence of relationships. Ex: P

str_relationships_rev(goobj)

Get a string representing the presence of absence of relationships. Ex: pr..

prt_keys(prt, pre)

Print the alias for a relationship and its alias.