I just noticed that the default values of Graph.dump_nodes() mentioned in the docs are different than what the code acutally does.
From the python docs:
> G.dump_nodes?
...
verbose: bool = True
Wether to show a loading bar while writing to file.
separator: str = '\t'
What separator to use while writing out to file.
header: bool = True
Wether to write out the header of the file.
nodes_column_number: int = 0
The column number where to write the nodes.
nodes_column: str = "id"
The name of the column of the nodes.
node_types_column_number: int = 1
The column number where to write the node types.
node_type_column: str = "category"
The name of the column of the node types.
At least I assumed those are defaults specified after the parameter names.
Turns out that if you run
# Just using Hetionet as an example here
from grape.datasets.hetionet import Hetionet
G = Hetionet()
G.dump_nodes('/tmp/node.tsv')
you actually get this:
> head /tmp/nodes.tsv
node_name
Anatomy::UBERON:0000002
Anatomy::UBERON:0000004
...
...
whereas I'd expect (from the defaults):
id category
Anatomy::UBERON:0000002 Anatomy
...
the nodes_column defaults to node_name instead of id
the node_type_column is supposed to default to category, but the node type column is missing altogether
Not a big issue, but confusing behavior at first!
Thanks for this great software package!!
Hi,
I just noticed that the default values of
Graph.dump_nodes()
mentioned in the docs are different than what the code acutally does. From the python docs:At least I assumed those are defaults specified after the parameter names.
Turns out that if you run
you actually get this:
whereas I'd expect (from the defaults):
nodes_column
defaults tonode_name
instead ofid
node_type_column
is supposed to default tocategory
, but the node type column is missing altogetherNot a big issue, but confusing behavior at first! Thanks for this great software package!!