Charles Tapley Hoyt cthoyt

## generate_literals.py
"""
Author: Charles Tapley Hoyt (@cthoyt)
License: MIT
See related blog post at https://cthoyt.com/2020/12/07/generating-literal-datasets.html
"""

from typing import Any, List, TextIO, Tuple, Type, Union

import click
import torch

## npa_xeno_example.csv
Experiment1.m5_node_label,Experiment1.m5_fold_change,Experiment1.m5_tstats
COX1,0.0442820351919402,1.27430203477638
ATP6,0.0829436812093022,2.86171297191134
SCGB1A1,-0.0829577087977886,-2.31945514137341
BPIFB1,0.303399473563391,7.82213833931689
RPL41,-0.0316199085257711,-1.3019865836353
ND2,0.0609064988662182,1.5913565091562
HBB,-0.60815873574393,-2.82215934759009
SCGB3A1,-0.114966188117398,-1.12153734714022
EEF1A1,-0.0856593570605189,-2.61018187225134

## make_mapping.py
import json
import sys

import click

import bioregistry


@click.command()
@click.option('--output', default=sys.stdout)

## create_obofoundry_issues.py
"""

This script blasts all of the OBO Foundry Repositories with a given issue.
Use sparingly.

 ______________________________
/ with great power comes great \
\ responsibility               /
 ------------------------------
        \   ^__^

## github_has_topic.py
from typing import Optional

import requests


def has_topic(owner: str, repo: str, topic: str, token: Optional[str] = None) -> bool:
    """Check if the given GitHub repository has the given topic.

    :param owner: The name of the owner/organization for the repository.
    :param repo: The name of the repository.

## pykeen_model_tweeterator.py
"""Generate PyKEEN model tweets."""

from textwrap import dedent

import click
from docdata import get_docdata

from pykeen.models import model_resolver


## bioregistry_formatter_trailing_slashes.py
import tabulate

import bioregistry


def main():
    """Generate a curation sheet for URL format strings with problematic trailing slashes."""
    rows = []
    for prefix, resource in bioregistry.read_registry().items():
        format_url = resource.get_format()

## download_reactome.py
from pathlib import Path

import pandas as pd

import pybiopax

ALL_PATHWAYS = "https://reactome.org/download/current/ReactomePathways.txt"


def download_reactome(directory):

## pykeen_uncertainty_demo.ipynb

      
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                PyKEEN Uncertainty Demo
              
          
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## wd-publication-ego.sparql
#defaultView:Graph

SELECT ?s ?sLabel ?rgb ?edgelabel ?o ?oLabel
WHERE {
  {
    SELECT ?s ?sLabel ?rgb ?o ?oLabel
    WHERE {
      ?o wdt:P50 wd:Q47475003, ?s .
      FILTER (?s != wd:Q47475003)
      OPTIONAL {
	"""
	Author: Charles Tapley Hoyt (@cthoyt)
	License: MIT
	See related blog post at https://cthoyt.com/2020/12/07/generating-literal-datasets.html
	"""

	from typing import Any, List, TextIO, Tuple, Type, Union

	import click
	import torch
	Experiment1.m5_node_label,Experiment1.m5_fold_change,Experiment1.m5_tstats
	COX1,0.0442820351919402,1.27430203477638
	ATP6,0.0829436812093022,2.86171297191134
	SCGB1A1,-0.0829577087977886,-2.31945514137341
	BPIFB1,0.303399473563391,7.82213833931689
	RPL41,-0.0316199085257711,-1.3019865836353
	ND2,0.0609064988662182,1.5913565091562
	HBB,-0.60815873574393,-2.82215934759009
	SCGB3A1,-0.114966188117398,-1.12153734714022
	EEF1A1,-0.0856593570605189,-2.61018187225134
	import json
	import sys

	import click

	import bioregistry


	@click.command()
	@click.option('--output', default=sys.stdout)
	"""

	This script blasts all of the OBO Foundry Repositories with a given issue.
	Use sparingly.

	______________________________
	/ with great power comes great \
	\ responsibility /
	------------------------------
	\ ^__^
	from typing import Optional

	import requests


	def has_topic(owner: str, repo: str, topic: str, token: Optional[str] = None) -> bool:
	"""Check if the given GitHub repository has the given topic.

	:param owner: The name of the owner/organization for the repository.
	:param repo: The name of the repository.
	"""Generate PyKEEN model tweets."""

	from textwrap import dedent

	import click
	from docdata import get_docdata

	from pykeen.models import model_resolver
	import tabulate

	import bioregistry


	def main():
	"""Generate a curation sheet for URL format strings with problematic trailing slashes."""
	rows = []
	for prefix, resource in bioregistry.read_registry().items():
	format_url = resource.get_format()
	from pathlib import Path

	import pandas as pd

	import pybiopax

	ALL_PATHWAYS = "https://reactome.org/download/current/ReactomePathways.txt"


	def download_reactome(directory):
	#defaultView:Graph

	SELECT ?s ?sLabel ?rgb ?edgelabel ?o ?oLabel
	WHERE {
	{
	SELECT ?s ?sLabel ?rgb ?o ?oLabel
	WHERE {
	?o wdt:P50 wd:Q47475003, ?s .
	FILTER (?s != wd:Q47475003)
	OPTIONAL {