cthoyt

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()

cthoyt

"""Generate PyKEEN model tweets."""

from textwrap import dedent

import click
from docdata import get_docdata

from pykeen.models import model_resolver

cthoyt

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.

cthoyt

"""

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

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

cthoyt

import json
import sys

import click

import bioregistry


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

cthoyt

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

cthoyt

"""
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

cthoyt

cthoyt

BioGRID Identifiers Problem, Solved

The file I included here has a set of organisms in the BioGRID identifiers download (version 3.5.184), latest as of time of writing on 2020-04-17) whose ORGANISM_OFFICIAL_NAME is not correct. I went and mapped these all with a mixture of synonym search on NCBITaxon and manual intervention. Each has the taxonomy identifier, so it can be used to get the most up-to-date information.

I would highly suggest including a taxonomy ID in this dump as well as the name, so it can be programatically mapped for anyone trying to integrate this

cthoyt

Charlie's PhD, The Drinking Game

How to play:

1. Read Charlie's PhD thesis... or just skim through it looking for fun
2. Drink based on the following rules:

1 Sip

• Charlie uses too many references